The startup code to initialize a mapper usually sits in the same page as the vectors. I dunno if that's the problem, though.

Have you tried putting something like:
here: JMP here

in the IRQ routine? You might be able to see where it went wrong if you can stop it early and trace backwards (easier said than done, heh) from the real return address.

At any rate, the CPU must've hit a BRK or CLI instruction somewhere. Interesting project, BTW. :)