There´s some game in which a timer keeps running even when paused (breakpoint etc).
How come? It´s offline. A ram writes seems to do nothing either. Not tried using ASM yet. :P
Have you tried different hooktypes?
Just VBI so far.
There are certain timers that continue to run in the system during a breakpoint. One of them is in the PPC, several others can be accessed through the GameCube style interface (see YAGCD).
One of these timers is how the Metroid protection worked. I'm not sure it can be properly stopped. I think I once tried to get Gecko.NET to be able to stop the time base register (I think that's what it's called), but it caused all kinds of flakey behavior. Your best bet is to hack at the code that reads the timer.
^