It's months since my last back-up

but something has happened to stop synchronize in the middle of reading directories - stops counting at about 68,000 directories when there are nearly 90,000 all together. Only task manager will kill it. I have run check disk on source and target and all is OK.
Is there any limit to the number of files/directories which can be compared with the synchronize utility? Or something else that may be causing this?
Win 7 x64 synchronizing from C: to a USB drive.