It has often been reported that CD-R's with dark colored bottoms won't work in any 3DO system. I can personaly attest to Verbatum brand discs refusing to work in either a 3DO or Sega CD. I've had the best luck with Memorex, Fuji, and Durabrand discs.
Another possibility is a bad burn. When I was using Imation discs, if I burned a 3DO game over 4X speed, it would be a bad burn. (Then again, I think burning ANYTHING at over 4X will result in a bad disc when using Imation... Nero even displays this nifty message about "changing write speed to 4X due to poor media.") Try making a direct copy of any 3DO game you already have at 2X. That will eliminate all the variables and you can work from there to find the best method to use for future burns.