Does NVRAM, PRAM or SMC have anything to do with the red light on a Riser lighting up but then not lighting up after a reseat and riser switch? One of the red leds for dimm 3 raiser b lit up red on my MacPro early 2008 lit up, so I reseated the ram in question on it by switching it with it's counter part (swapped dimm 3 for dimm 4) and switched it from the top to the bottom riser.   Then I had the full amount of RAM again and no red light.  

I also run Ubuntu 16.04 LTS on it.  

I have never reset the nvram, pram, or SMC on it, and so I was wondering if that is somehow related to such strange events in the hardware as the led lights coming on and going away after reseating the ram as I did.
As you may know, the Non-Volatile RAM (NVRAM) and System Management Controller (SMC) have totally different purposes. 

In terms of the red light you're referring to:


resetting the NVRAM will have absolutely no bearing on this whatsoever
resetting the SMC could have an influence, but probably not in the way you're asking about. 


At its core the SMC is responsible for power management and controlling the thermal environment of your Mac. Typically this covers things like interpreting and responding to various sensors, battery charging, sleep/wake/hibernation, the power button and restarts/shutdowns, LED indicators, and so on.

Since the red light needs a power source, as do RAM chips to operate, it's quite possible that resetting the SMC could have an impact on the light:


directly in terms of its own power source
indirectly because the associated RAM isn't getting the power it needs and therefore triggers ECC errors which triggers the red light.


However, despite the above explanation, in most cases a red light indicates nothing more than the fact the RAM isn't seated properly. Removing and reseating the riser(s) will usually rectify this problem. While it may seem unlikely that this was the problem in your case, it actually doesn't take much for this to occur (e.g. the computer is moved, bumped, etc).