Do you active copy many folders? Or do you have a big list of files in the remote access list of the pogoplug software?
Myself using OSX 10.6.6 I haven't encountered the exact issue you describe.
But after copying files to a certain folder this folder doesn't update it's contents. I need to go to the web interface to see the files I have just copied to that particular folder. I'm using Pathfinder, Finder and Forklift all three side by side... this might have something to do with it.
The software constantly beachballs and slows finder to a crawl until you can't even view your own file system unrelated to pogoplug. This is a huge annoyance. It is practically unusable.
It seems like the older version of the software used a local connection to move files and the beta does not as larger files seem to be taking a lot longer to move to a pogoplug drive.
I have also had a lot of crashes especially when it prompts me if I want to replace a file or folder.
After further testing it does not happen on my older macbook, but it does happen on my new 2011 Macbook Pro. Don't know why. I turned off active copy, and it is painfully slow and beachballs finder every time. Switched back to original on that computer.
Are you referring to the Pogoplug Beta (server) or to the PogoPlug Client for OS X? I have tons of problems with the BBOD when doing anything related to pogo drives when the drive on the pogo (hardware) is formatted NTFS. I reformatted the drive to EXT3 (linux) and my BBOD problems have gone away.
I think @hbkdinobot is referring to the client?! Right? Your answer might be here:
http://www.pogoplugged.com/forum/thread/16100/100-CPU-on-OSX-10.6.7/
Anyway this is what worked for me.
Good luck!

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It seems to be even worse on my new 2011 Macbook Pro.