not sure if you figured out how to fix it. generally when i have this problem on linux, I have the app write to a symlink rather than a mountpoint.
E.g. If JungleDisk is writing to /Volumes/SpareDrive (which is the mountpoint) and it creates a SpareDrive directory when the drive is not connected, I'd do this:
sudo ln -s /Volumes/SpareDrive /Users/Shared/SpareDrive
Then have JungleDisk write to /Users/Shared/SpareDrive instead. When JungleDisk write to /Users/Shared/SpareDrive when /Volumes/SpareDrive is not mounted, it'll just throw an error (symlink target doesn't exist) instead of creating the folder.