Worst case scenario is that there are writes happening outside of VBlank.  This could explain all the problems:

1) The PPU updates the VRAM address as it runs.. therefore if the game sets the address to $2000 then writes to VRAM, it may actually be attempting to write to $2001 or higher if the PPU modified the address at all (creating garbage)

2)  The Debugger might not snap on such a breakpoint because the debugger may not run the PPU (to update the VRAM address) before it checks the address against the desired ranges.  IIRC, FCEUXD snaps its breakpoints before the instruction is even executed -- FCEU probably doesn't catch up the PPU (and thus, modify the VRAM address to what it "should" be) until after the write is processed (and thus -- after the instruction is executed).


Check to see *when* the game is writing to VRAM.  Make sure it's not after rendering has started.  Try to optimize as much VBlank code as you can.



But that's all speculation.  The problem might be something else entirely, you never know.  Although this is the only explanation I can think of that would explain your breakpoints failing.