This is only a theory, mind you, but I think the reason may be with the order in which the data is put on the CD. PC Engine CDs have track 1 as an audio warning that the CD is a PC Engine CD, track 2 is the actual game data, and tracks 3+ is the CD audio. I've always wondered if this confuses the CD-ROM drives in some way.
On a side note, I notice that all of the recent CD/DVD-ROM drives that I have won't read past the first track of my PC Engine CDs, while my old CD player can still access all the audio tracks. I've been wanting to rip all the BGMs from my various PC Engine games, but don't have a single computer that will cooperate with me.