This is only happening with zsnes, whether I use the gamepad or the keyboard. The problem is that the controls seem to work at random, sometimes they work and sometimes they don't, although I doubt it has anything to do with my hardware, but I'll tell you just in case (this is my first post here)

CPU: AMD Turion(tm) II P540 Dual-Core Processor
Graphics Card: AMD M880G ATI Mobility Radeon HD 4250
RAM: 4 GB (3.74 Usable)
64-Bit Operating system
Windows 7

Version: Zsnes V1.51

The controls seem to be enabling and disabling at random, at first I thought the connection with the gamepad was poor, but then I realised the same problem was with the keyboard (yes, I did configure the controls).