I am using the msbuild parser. I will attach one of the log files.
There is only one copy of the msbuild.log file and the search path I use is **/build/msbuild.log
Console log parsing is unchecked.
[WARNINGS] Parsing warnings in files: **/build/msbuild.log
[WARNINGS] Successfully parsed file E:\hudson\jobs\Network Discovery\workspace\KND\build\msbuild.log of module build with 150 warnings.
Those are the only 2 [WARNINGS] lines in the log.
It started happening after I upgraded hudson, but I do not know from which version to which. 
Which parsers are you using?
Can you please attach one of the parsed log files (with expected #warnings)?
Is there any chance that the file with the warnings is found twice in your workspace? The plug-in counts the totals based on the found warnings, however the breakdown uses a set which eleminates dplicates.