I'm aware of the FTP hang problem, but if you wait for like 30seconds - 1min it will quit. I'll take a look at it later. Also I think - exitting with the [PS] button doesn't cause such hang.
About the doubling - try to download the version from the first post again and re-install it.
Try to use the default search paths and have in mind that if you have a game in more than one location - you will see it multiple times (like if you have the same game backup from different managers).
# Look for game backups recursively in these folders:
# (leave blank for USB (usb_home) root (/) folder)
# Main search folders:
# Secondary search folders:
or better add the full path to home3/4/5
or whatever you use.