Upgraded my Jenkins instance (to version 1.611).
Tried to upgrade fitnesse plugin also from 1.8 to 1.12.

Results from version 1.2 (works)
...
Reading results as windows-1252 from D:\WS\master\Reports\fitnesse\fitnesse_results.xml
Parsing results...
Got results: null (): 1650 right, 0 wrong, 0 ignored, 0 exceptions
Archiving artifacts
.....

Build fails on Version 1.13:
Reading results as windows-1252 from D:\WS\master\Reports\fitnesse\fitnesse_results.xml
Parsing results...
Write fitnesse results to: D:\Apps\Jenkins\jobs\Master Build\builds\7995\
javax.xml.transform.TransformerException: java.lang.NumberFormatException: For input string: ""
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(Unknown Source)
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(Unknown Source)
at hudson.plugins.fitnesse.NativePageCountsParser.transformRawResults(NativePageCountsParser.java:26)
at hudson.plugins.fitnesse.NativePageCountsParser.parse(NativePageCountsParser.java:19)
at hudson.plugins.fitnesse.FitnesseResultsRecorder.getResults(FitnesseResultsRecorder.java:142)
at hudson.plugins.fitnesse.FitnesseResultsRecorder.getResults(FitnesseResultsRecorder.java:119)
at hudson.plugins.fitnesse.FitnesseResultsRecorder.perform(FitnesseResultsRecorder.java:77)
at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:45)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:764)
at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:724)
at hudson.model.Build$BuildExecution.post2(Build.java:185)
at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:671)
at hudson.model.Run.execute(Run.java:1769)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:374)
Caused by: java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at hudson.plugins.fitnesse.NativePageCounts.startElement(NativePageCounts.java:68)
at com.sun.org.apache.xml.internal.serializer.ToXMLSAXHandler.closeStartTag(Unknown Source)
at com.sun.org.apache.xml.internal.serializer.ToSAXHandler.flushPending(Unknown Source)
at com.sun.org.apache.xml.internal.serializer.ToXMLSAXHandler.endElement(Unknown Source)
at com.sun.org.apache.xml.internal.serializer.ToXMLSAXHandler.endElement(Unknown Source)
at GregorSamsa.template$dot$0()
at GregorSamsa.applyTemplates()
at GregorSamsa.applyTemplates()
at GregorSamsa.transform()
at com.sun.org.apache.xalan.internal.xsltc.runtime.AbstractTranslet.transform(Unknown Source)
... 16 more
---------
java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at hudson.plugins.fitnesse.NativePageCounts.startElement(NativePageCounts.java:68)
at com.sun.org.apache.xml.internal.serializer.ToXMLSAXHandler.closeStartTag(Unknown Source)
at com.sun.org.apache.xml.internal.serializer.ToSAXHandler.flushPending(Unknown Source)
at com.sun.org.apache.xml.internal.serializer.ToXMLSAXHandler.endElement(Unknown Source)
at com.sun.org.apache.xml.internal.serializer.ToXMLSAXHandler.endElement(Unknown Source)
at GregorSamsa.template$dot$0()
at GregorSamsa.applyTemplates()
at GregorSamsa.applyTemplates()
at GregorSamsa.transform()
at com.sun.org.apache.xalan.internal.xsltc.runtime.AbstractTranslet.transform(Unknown Source)
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(Unknown Source)
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(Unknown Source)
at hudson.plugins.fitnesse.NativePageCountsParser.transformRawResults(NativePageCountsParser.java:26)
at hudson.plugins.fitnesse.NativePageCountsParser.parse(NativePageCountsParser.java:19)
at hudson.plugins.fitnesse.FitnesseResultsRecorder.getResults(FitnesseResultsRecorder.java:142)
at hudson.plugins.fitnesse.FitnesseResultsRecorder.getResults(FitnesseResultsRecorder.java:119)
at hudson.plugins.fitnesse.FitnesseResultsRecorder.perform(FitnesseResultsRecorder.java:77)
at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:45)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:764)
at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:724)
at hudson.model.Build$BuildExecution.post2(Build.java:185)
at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:671)
at hudson.model.Run.execute(Run.java:1769)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:374)
Build step 'Publish Fitnesse results report' changed build result to FAILURE
Build step 'Publish Fitnesse results report' marked build as failure
Archiving artifacts

The result set is large.
I had a similar error in the past with the html publisher plugin and large files (that was fixed at some point in that plugin)

I had to revert to 1.8 to get it to run again.