Yeah, those RAM Riser boards aren't a real smart design IMO. Probably due to the component grade selected for the line assembly. I had a similar issue with a 2006 MP myself. Many times when removing and reinstalling those riser boards for cleaning, testing RAM, or whatever, the initial first few cold starts would produce red lights and the system wouldn't recognize the RAM on that card. 1 to 3 reseats later and it's all good. This tells me that the parts used (probably the card thickness and the mainboard headers) are NOT of optimal quality and/or tolerance levels.
To clean the landings on the mainboard's headers use acetone and a cotton ear swab. lightly (and I really mean lightly) dampen the swab in pure acetone. Place it between two of the landing surfaces and rotate R&L a few times. Repeat for about 3 or 4 landing sets and then grab a new swab even if it doesn't look dirty.
When done examine the card edge connector on the riser board itself. If you see any scratches or marks at all get yourself a pink pencil eraser (not the white rubber ones) and rub down those contacts. Apply about the same pressure you would when erasing pencil marks off paper - assuming you weren't one of those kids who constantly turning in papers with eraser holes in the paper.
When done use a tissue paper and some of that acetone and wipe down the card edges with it.
Reassemble and have a go. You might even still need to reseat the card once or twice. If that doesn't fix it then I would move to RAM testing before considering a mainboard replacement!
Assumming you have 8-cores The fastest way to actually test for bad memory beyond Apple's initial check, is to download
Rember, duplicate it the number of times you have CPUs (one copy per core), open one and enter RAM/Cores (8GB ÷ 8?), set that much minus about 5MB in the setting window, turn OFF "Continue on error" and set "Quit All Apps" and "Quit Finder" in the preferences, quit and then open all 8 instances (which should now all use those settings), and then just start them off. If it appears to be chugging too slowly or if one Rember instance seems almost stuck, stop (don't quit) that one and give it less RAM to do - a little at a time till it takes off normally.
When you test the memory use Apple's default SMC system cooling profiles. If you have SMCFanControl installed set it to the installation preset called Default - which will allow Apple to have their way and let the RAM heat up to their idea of operating temperatures - which is better when testing for bad memory.
