This is pretty rare to see, but I had something similar happen to me once. I burned a copy of Ys 4 translated onto a cheap Maxell CD-R... Loading was SO SLOW and often it would load corrupt data-- small graphics were garbled and text boxes would be filled with gibberish *#($&$@! stuff... You could really hear the drive struggling to read the disc, too.
I would guess that you're having a similar issue and it has something to do with the CD-Rs... Reading a CD-R in one of these old CDROM2 drives is like reading a badly scratched up original... The pits in the disc of a CD-R aren't so perfectly defined like in a factory-pressed disc... So you could say they appear 'blurrier' to the laser pickup and it has a harder time distinguishing the 1s and 0s.
Your drive might benefit from a pot tuneup. That might help the drive read a bigger variety of discs. I usually start off with a factory pressed disc, like a music CD, and adjust the pots until it reads perfectly and skip recovery works good. Then I will change to a good quality CD-R and adjust again. Then I will change to a crappy quality CD-R and adjust one more time. But be warned... THIS CAN BE A VERY FRUSTRATING EXPERIENCE TO DO BY 'EAR' (without an oscilliscope). You could spend hours or even days adjusting the pots and still end up making it worse. But if you get it tuned just right-- It should be somewhat tough to get an original factory-pressed disc to skip by tapping on the drive... While CD-Rs will skip much easier, the skip recovery should work most of the time.
Also some drives just plain work better than others with CD-Rs. Newer drives especially have better tolerance when reading CD-R. **On a side note... Great idea using an old CD burner to burn the discs. I've noticed my older burner seems to do a better job for these picky consoles, too.**