Two things:
1) Yes, anti-virus/anti-malware programs can hinder the proper operation of an executable, dll, etc as it's their inherent function. All they have to do is suspect one is a possible threat and bang.
2) ANY program can affect another if it's poorly written. If you have something with a memory leak, etc. it could very easily be affecting another running program's memory, interrupt, DMA, etc. access. It's basically out of control. And it may not be noticed by other programs because they aren't using those resources affected by the 'bad code'.
Stripping the startup of a PC to bare bones is a common way to sort out conflicts.
And it could be a lousy mouse, soundcard, and/or graphics driver, easily.