Controller not working for some games ?

Hello everyone!
After years of waiting I have my NES emulator almost working!
I encountered an interesting problem though.

For roms like Zelda 2 and Castlevania 1 everything works fine.
For Zelda 1 and Megaman 2, the buttons seems warped (if I press right it read as start) ?!?!?

Also the allpads test rom shows that it reads all the button pressed.

I doubt it is the logic itself of the controller, I am more sure about some collateral effects from APU and such.

Has anyone ever saw something like that ?

Thank you a lot!

And of course it is me, but somewhere else.
The absolute Y addressing mode was always adding a dummy read, thus interleaving the reads (was reading 16 times instead of 8)!

Did you run nestest CPU test? I have problems with controller as well but nestest run's 100% flawlessly for me