I am running the Windows version of KSP natively in Windows (Windows 7 Ultimate SP1 x64), so I can't comment on that (it sounds like another issue).
However, to my ears the it clearly indicates the wrong use of some type of lossy audio compression. My guess would be that the audio encoding bit rate for the audio assets was set too low during code packaging.
When I moved from version 1.0.5 to 1.1.x it was immediately apparent while listening to the start-up theme, but all music (and probably other audio) is affected.