I had the same problem on underpowered small machine, and enabling Case Sensitive FS, solved the problem.
The difference in performance was:
A) +1day
B) ~ 10 minutes (after enabling CSFS)
This is VERY COSTLY check 
I had the same problem on underpowered small machine, and enabling Case Sensitive FS, solved the problem.
The difference in performance was:
A) +1day
B) ~ 10 minutes (after enabling CSFS)
This is VERY COSTLY check