I aquired 2 MacPro A1186 one quad 2.66 12mb and one quad 3.0 16mb same brand of memory.
Upon simultaneous power up for some reason the 2.66 reaches the boing sound quicker and boots to GUI in 32 sec while 3.0 boots in over a minute. Both have fresh install of Yosemite.
Swapped the HD and still the same.
I also reset SMC and PRAM on 3.0 and still the same.
Geekbench 32bit multiprocessor 3.0 scored 56xx and 2.66 51xx which seems to be normal.