I don't know whether that's true, but sometime from now (maybe since I've started using ubuntu 11.04), my music files have started showing errors on the execution. Basically, many .mp3 files I had are damaged and start the music twice, like: the music starts then 2 seconds later it restarts and continues playing. This errors appear when listening to the songs in any players, being from ubuntu, windows or iPod. Is it possible that Banshee is doing this?
Banshee should not be damaging your files as it should be merely reading them. Unless there is something (extremely) wrong with how the metadata is being written back into the mp3 files.
Go to Edit >> Preferences and see if the record metadata to files box is checked. If it is, try disabling it. If it is disabled, than it is unlikely Banshee is causing it.
You mention starting to use ubuntu 11.04 - did you do a clean install or a direct upgrade? An upgrade could represent an issue with audio drivers. I'm baffled because you mention trying it in ubuntu, windows and the iPod.
Have you done any sort of re-enconding/conversion of the files?
What you can do to test is first testing an album in windows and then trying in ubuntu (and vice-versa).
There are so many factors in to question that I ultimately think you are better off filing a bug report over Banshees launchpad. https://bugs.launchpad.net/ubuntu/+source/banshee