My suspicion is, that the issues does not directly come from the initialization, but rather that some program is expecting a specific state and after an IGR this state is not as it was before... This (alone) however would not explain, why this also happens to very few games, without an IGR and by going 'through' the hacked OSDSYS or letting the HDD startup before-hand.
...or something is left in RAM, like the hooked Kernel-Syscalls...
On another note (
@sp193): When I IGR, are the Kernel-Hooks still in place (or not)?! Does it have any effect, or is the Kernel(-RAM) flushed during a boot of rom0:/OSDSYS? Afaik it is not (flushed) or some TSR-Tools shouldn't work...
@Peppe90: Would you mind trying mode 3 on those games, which are compatible with it, but have issues with IGR? Does it change anything?
I suppose it does not, but it is worth a try!
It COULD have an influence and so it is worth some tests (IMO).