I'm having the same kind of issues with cart games, though I haven't really tested CD games that much for now. The problem is, I'm pretty sure I have a v. 2 device, given the date I got it (order ref. RPVYWYMQM).
Specifically, I've found game freezes (which force me to reset the system) on PC Genjin, Makyou Densetsu, Download, Kick Ball, Dragon Saber, Genpei Toumaden and Wonder Momo. The later three (Namco) games, just need to be left in demo mode for it to happen after some minutes (usually less than 30), but the others, I can't consistently reproduce them and indeed it's not the usual behaviour. I'm sure it happens in other games too since I've only tested a small part of the system's library. The roms I'm using don't have this issue with emulators, and the console is supposedly in good condition (PCE white). The in-game trigger is disabled. Super Darius (CD game) also freezes when you leave it in demo mode.
Is my v. 2 the only one suffering from this?
Makyou Densetsu / Wonder Momo