when i OGG one of the new psuedo-CDs (the ones that try to autorun a "no ripping" app, but easily disabled) every song has a millisecond or so of silence about 10 seconds into every song. it's quite noticeable. for a while i thought it was just the one CD (a dud maybe), but now i have a few copyprotected discs, and when ripped they ALL have this annoying millisecond of silence a few seconds into every song.
No idea...but the first thing I would try is ripping to wav first. If worst comes to worst, you could always become proficientat wav editing and just delete the silence.
You can also get a male -> male 3.5mm audio cable and run it from your sound card's line-in jack to your CD player and rip them that way so you won't have to edit squat. Only downside to this is the time required to do that.
i ran into the same problem when i was ripping music, then converting it to mp3 for my mp3 player. like 10 seconds of silence, then music. So i first converted the ripped music files to wav, edited out the silence, then converted that to mp3
I once heard a while ago that a lot of copy protection stuff is easily defeated by making a CD image of the CD, mounting said image, and ripping the audio off the virtual CD. Never had a chance to try it out myself, though.