Below are links to the NES fpga:

1) https://github.com/brianbennett/fpga_nes
Using Spartan 6 : Nexys 3
There is a glitch in one game that was discussed here:
http://forum.gadgetfactory.net/index.ph ... pistrello/

2) https://sites.google.com/site/ece31289u ... oratorio-3
Using Cyclone IV : DE0-Nano
Uses the same source codes in (1) but no glitch. Works nicely.

3) https://github.com/strigeus/fpganes (Luddes NES Blog)
Using Spartan 6 : Nexys 3 or 4?
Requires USB joystick on PC. Customized software to load games and joystick positions to FPGA.
I could not get either to work on Nexys 3.

Appreciate if anyone can help investigate the glitch in (1) ?

Is this the glitch in question?

Yes, that's the glitch. No glitch on the De0_Nano version.