Mac Pro Freezes momentarily and frequently

About a month ago my Mac pro started behaving strangely. It will freeze for 2-5 seconds where nothing appears to work. Sometimes the beachball spins, other times it doesn't. It does it in all applications. The screen doesn't change at all and there is no other visual clues except that sometimes the cursor turns to the pointing hand instead of the arrow. When the freeze ends the computer catches up to whatever I was doing before.

It's not a new computer - it's a first generation Mac Pro, but a year ago Apple replaced the mother board and the processors because it had been incorrectly repaired a few years earlier and some thermal paste had been omitted. The drives are all new and when this started I cloned the main drive to a new one to eliminate a hard drive failure as a possibility. I've run permissions checks both with the apple utility and Cocktail.

When we replaced the main board I replaced all the memory

So here's the specs of the system:

2 x 2.66 GHz Dual Core Xeon
16GB 667 MHz DDR2 FB-DIMM memory all from Kingston and all 2GB units and all slots used
ATI Radeon HD 5770 (new last year)
OSX 10.7.5 (the last update that would run on this machine)
None of the drives have more than 50% use

Other than being annoying it doesn't seem to have any other issue (data isn't being lost). Any suggestions would be welcome.

Not keen on Kingston memory or SSD's had them fail. OWC and Crucial recommended around here. Try removing all the memory and start off with 2x2GB modules and test them all out. Sounds like a memory problem.