Given the subversion tree:
/trunk/
/trunk/ends_with_t/
/trunk/foo/
/trunk/foo/file
/trunk/file

And the subversion module configuration
scheme://.../trunk/foo -> foo
scheme://.../trunk/ends_with_t -> ends_with_t

hudson.scm.SubversionChangeLogSet.LogEntry.getAffectedPaths() returns
runk/file
file

This is caused by hudson.scm.SubversionChangeLogSet.LogEntry.preparePath() when it uses all of the configured module locations to remove the common parts from file paths. "trunk/file" was not part of the change that was added to the filesystem. When findCommonParts( "trunk/ends_with_t", "trunk/file" ) is called, it returns "t" because that is the common tail of the folder that matches the beginning of the file path. pareparePath then calls substring on the file path with the length of the common part, which removes the "t" from "trunk/file".