Do you have a lot of hand history files?
If so, try running File > Setup Wizard to import all of your hands and move them to the Processed folder. (Alternatively check out the
Tutorial: Preventing Duplicates)
Auto Import isn't designed to handle a large number of files - it is designed to work with the files created while you're playing live.
If that isn't the situation, or that doesn't remove the problem, please enable logging and restart PT4. Reproduce the problem and then
report your problem so that we can investigate further.