I don't if anybody remembers complains about a MP3 decoding bug with Nero, which causes corrupted audio data in the decoded WAVE files. With the help of Nero's tech support we were able to track down the issue. It's not Nero's fault, it's caused by an interaction of MP3Pro.dll and the Pxhelp20.sys present on many systems. Somehow this driver screws the decoding process and the resulting WAVE files sometimes contains audible skipping.
So if you're having this problem, don't blame Nero anymore, like I did. Anyway an older MP3Pro.dll version was not affected by this issue, only newer ones.