CS4 Batch processing only processes half the files!

I scan 6x6 negs on an Epson scanner and when they are done they need to be rotated 90 degrees and flipped horizontaly. I set up an action to do this (Rotate, Flip, Save and Close) and everything was going swimmingly - then recently I've started having problems.
For example - I've scanned 60 images which I select in Bridge and then open them in PS CS4. I select Automate>Batch and then select my saved action and away it goes. PS chugs its way through the 60 photo's and closes them all (so it looks like they have all been processed), but when I go back to Bridge and it starts refreshing the thumbnails only 30 of them have been rotated and flipped. So then I select the remaining 30 images and batch process them - this time it only processes 15 and so on. This is really annoying as if I get down to around 9 images it won't process any of them!
Any ideas?
Cheers
Simon

Curt Y's comments sound good to me, too.
As a "test," try your action on a folder and check Bypass Open (that option should still be in CS4) and see if that handles all of the folder - after you take Curt's advice. Though Batch normally just Opens one at a time, and the computer should recover the resources used for that one on Close, it might not be happening for you.
Good luck, and let us know if anything works,
Hunt
Also, you might want to add your full system specs. if you still have the issue. I'd pay very close attention to the I/O sub-system, i.e. the HDD's, their speed, size, free space, controller type and how they are allocated on your system.

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