This posting is older than 6 months and can contain outdated information.
My best guess is that you have added a folder with deep structure to
the list of folders to be searched manually.
Did you add any search paths to Remote Buddy's Movie Library manually?
Can you still access Remote Buddy's interface on your Mac?
Which version of OS X are you running?
If possible, please also create an activity log (=> launch Activity
Monitor.app, select Remote Buddy, then click "Analyze") and cut and
paste it here or send it to the website's info email address.
Best regards,
Felix Schwarz