UI updates were forcibly disabled by application "xxx" for over 1.00 seconds
I am running a mid 2012 13" MacBook Pro and it has recently been locking up frequently. The console shows UI updates were forcibly disabled by application "xxx" for over 1.00 seconds, usually the culprit is the Finder. At first I thought it was an OS issue, so I reinstalled the 10.9.4 combo installation without any change. Then I ran disk repair and permissions repair from the boot utility, and neither gave me any errors. I then tried Safe Mode booting to see if it was an application, but the computer was still functioning noticeably slower. Next was single user mode with a FSCK which did not show any disk abnormalities. I was worried it was a disk issues so I ran SMART status as well without any errors being reported on the drive. I ran the comprehensive Apple Hardware Test and was normal. Finally I opened the bottom of the MacBook Pro to see if the SATA cable looked damaged but it was visibly intact without any obvious signs of damage, and then I disconnected the cable from the logic board and hard drive then re-attched it. That seemed to have improved things although only for maybe 20 minutes of use.
Given everything I have done, how can I better pinpoint what is causing this lag? I am not sure how much more the folks at the Apple Store can do.