Sounds to me like your hard drive has found a bad sector.

Normally this would be a sign of an HD that is starting to fail, but it can also be a sign of abnormal disk fragmentation.

If you have the time and inclination, try this:

1. Make a clone backup of your drive to an external HD. This will save you time later. If you're using Time Machine, let it make an up-to-the-minute backup as well.

2. Boot from the clone. Make sure everything seems to work properly.

3. Use Disk Utility to erase the boot drive. Choose the zero-out (ONCE!) option. The other ones take DAYS. Once is enough for what we're doing.

4. Either clone back from your clone backup, or do a restore from your TM backup.

That will effectively defragment the drive. If you're still getting the hangup after that, I'd say the drive is in trouble.