For historical reasons Windows filesystem is case insensitive (unfortunately). Although the filesystem does store case, frequently the users don't have control over the case of created file/folder names.
Windows users expect all tools to be case agnostic. However, this is not the current situation with Jenkins.
For example, for ArtifactDeployer Plugin on Windows, setting "Artifacts to deploy" to "Foo/**" will deploy nothing if the filesystem folder is called "foo". This is clearly not a behaviour Windows user would expect. Similar issue happens with JUnit Plugin.
The problem root is in the usage of Ant FileSet class which is by default case sensitive (although it can be set to ignore case).