When I run a PA in the RMS Console it takes 1.5 hrs to complete on roughtly 2000 servers located worldwide. My QE infrastructure is pretty well tuned utilizing distribution groups and 160+ query engines.
When I run a PA using the CCS Stds module, it takes over 15hrs just for the data collection alone.
I have a distributed CCS infrastructure. Separate Directory Server, App Server, DPS, BVIS and SQL Server.
All of my MQEs/SQEs/BVIS/ECS are patched to 10_5_PCU_2011-2 level
One thing I did just read on the 10_5_PCU_2011-2 update is that the data collection piece needed to be updated before the Reporting/Analytics piece. I did not do in that order so it might be my problem. I am going to rerun the R/A update again now that the D/C portion is current and see if that helps. Following the intall path of Directory server first, then App Server, followed by DPS.
I will know more next week as to whether or not it helps.