I am having the same issue. I have found a way around but it isn't for people uncomfortable with command line.
I will start by mentioning what I believe to be the cause for the issue. When the Almond plus reboots the torrent client starts before the mount point for the USB is created. So since there is nothing in /mnt/usb/%mounted drive% where the torrent client is supposed to look for configurations it creates that path and sets up the default file structure. So now there is a /mnt/usb/%mounted drive%. THEN the USB drive tries to mount and since /mnt/usb/%mounted drive% already exists it creates/mnt/usb/%mounted drive%_2 or so on.
Now the fix.
1) Disable the torrent client (so it wont auto create /mnt/usb/%mounted drive%
2) Shutdown the Almond plus
3) Remove the USB drive
4) Start the Almond plus
5) Log into the Almond plus with SSL
6) Delete the folder /mnt/usb/%mounted drive% (rm -rf /mnt/usb/%mounted drive%)
7) Plug USB drive into Almond plus
Enable the torrent client
^Happy accident
I give no warranties for following my instructions but it has worked for me on multiple occasions.
I hope one of the programers will see this and fix the start order of the Almond plus