Yeah, the 8042 is the keyboard controller chip in the original PC specification. I think the same features are buried in the motherboard chipset now.
I can't think of anything that would make this fail aside from some wierd low-level conflict. For example, if you are having memory problems it can show up as almost anything, because just about everything reads and writes values to memory. If one of those values comes back wrong it can cause the software to fail.
Obvious question: does the problem go away if you revert to the old memory?
Also, beep code documentation isn't always right, and interpreting the beep codes themselves can be confusing.