I just tried the 'find' command suggestion, and found that the exact same thing is happening. different results each time.
So i guess its not a perl issue, but if anyone has any suggestions im open too them.
One thing i found is that if I run the script back to back to back, really fast, i get the same results. but if i wait a few min, or do other things on the system inbetween, the results are different.
Again, im positive the directory contents are NOT changing.