Could you be a bit more specific please? How are they discarded 'in a wrong way' - are too old or too new builds being discarded?

please see the screenshot:
builds 3-9 are missing in the "Build History" list, therefor I assume it's discarded due to 30 days configuration

There are other reasons why builds could be deleted. The code for deleting old builds is basically unchanged for years, so I would be surprised when a bug should show up now.
Do you have any more information - e.g. did you have logging enabled in FINE level?

seems you're right and it's not related to 30 days discard setting.
As I got some lost builds again (not on year change). Problem seems to be present that whenever I restart my PC some builds get lost.

See attached log file as well as one of the reffered problematic build.xml files for details:
/var/log/jenkins/jenkins.log -> jenkins.log
/var/lib/jenkins/jobs/yourpresenter/builds/2012-01-01_21-39-54/build.xml -> build.xml

Hope it helps in further analysis.

I checked the log file and there is exception thrown:
hudson.util.IOException2: Unable to read /var/lib/jenkins/jobs/yourpresenter/builds/2011-12-31_12-32-47/build.xml
at hudson.XmlFile.unmarshal(XmlFile.java:160)
at hudson.model.Run.reload(Run.java:283)
at hudson.model.Run.<init>(Run.java:272)
at hudson.model.AbstractBuild.<init>(AbstractBuild.java:162)
at hudson.maven.AbstractMavenBuild.<init>(AbstractMavenBuild.java:54)
at hudson.maven.MavenModuleSetBuild.<init>(MavenModuleSetBuild.java:137)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at hudson.model.AbstractProject.loadBuild(AbstractProject.java:949)
at hudson.model.AbstractProject$1.create(AbstractProject.java:256)
at hudson.model.AbstractProject$1.create(AbstractProject.java:254)
at hudson.model.RunMap.load(RunMap.java:221)
at hudson.model.AbstractProject.onLoad(AbstractProject.java:254)
at hudson.maven.MavenModuleSet.onLoad(MavenModuleSet.java:617)
at hudson.model.Items.load(Items.java:115)
at jenkins.model.Jenkins$14.run(Jenkins.java:2360)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:146)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:259)
at jenkins.model.Jenkins$5.runTask(Jenkins.java:800)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:187)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:94)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)
Caused by: com.thoughtworks.xstream.converters.ConversionException: Cannot deserialize object with new readObject()/writeObject() methods
---- Debugging information ----
class : hudson.maven.MavenModuleSetBuild
required-type : org.eclipse.jgit.lib.ObjectId
path : /hudson.maven.MavenModuleSetBuild/actions/hudson.plugins.git.util.BuildData/buildsByBranchName/entry/hudson.plugins.git.util.Build/revision/sha1
line number : 15
-------------------------------
at com.thoughtworks.xstream.converters.reflection.SerializableConverter.doUnmarshal(SerializableConverter.java:281)
at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:162)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at hudson.util.RobustReflectionConverter.unmarshalField(RobustReflectionConverter.java:290)
at hudson.util.RobustReflectionConverter.doUnmarshal(RobustReflectionConverter.java:233)
at hudson.util.RobustReflectionConverter.unmarshal(RobustReflectionConverter.java:180)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at hudson.util.RobustReflectionConverter.unmarshalField(RobustReflectionConverter.java:290)
at hudson.util.RobustReflectionConverter.doUnmarshal(RobustReflectionConverter.java:233)
at hudson.util.RobustReflectionConverter.unmarshal(RobustReflectionConverter.java:180)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at com.thoughtworks.xstream.converters.collections.AbstractCollectionConverter.readItem(AbstractCollectionConverter.java:71)
at com.thoughtworks.xstream.converters.collections.MapConverter.populateMap(MapConverter.java:79)
at com.thoughtworks.xstream.converters.collections.MapConverter.unmarshal(MapConverter.java:66)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at hudson.util.RobustReflectionConverter.unmarshalField(RobustReflectionConverter.java:290)
at hudson.util.RobustReflectionConverter.doUnmarshal(RobustReflectionConverter.java:233)
at hudson.util.RobustReflectionConverter.unmarshal(RobustReflectionConverter.java:180)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at com.thoughtworks.xstream.converters.collections.AbstractCollectionConverter.readItem(AbstractCollectionConverter.java:71)
at hudson.util.RobustCollectionConverter.populateCollection(RobustCollectionConverter.java:85)
at com.thoughtworks.xstream.converters.collections.CollectionConverter.unmarshal(CollectionConverter.java:61)
at hudson.util.RobustCollectionConverter.unmarshal(RobustCollectionConverter.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at hudson.util.RobustReflectionConverter.unmarshalField(RobustReflectionConverter.java:290)
at hudson.util.RobustReflectionConverter.doUnmarshal(RobustReflectionConverter.java:233)
at hudson.util.RobustReflectionConverter.unmarshal(RobustReflectionConverter.java:180)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:82)
at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:63)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:76)
at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:60)
at com.thoughtworks.xstream.core.TreeUnmarshaller.start(TreeUnmarshaller.java:137)
at com.thoughtworks.xstream.core.AbstractTreeMarshallingStrategy.unmarshal(AbstractTreeMarshallingStrategy.java:33)
at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:926)
at hudson.util.XStream2.unmarshal(XStream2.java:91)
at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:912)
at hudson.XmlFile.unmarshal(XmlFile.java:156)
... 25 more

Looks like a duplicate of JENKINS-12267