According to the JFUploader backend:
If a user is assigned to more than one group then the one with the highest id is used. Normally this groups are the ones created by yourself which gives you the most flexibility.
(this is for the Master profile directory mode option)
My account belongs to 2 groups (Manager and fpdr), but when I uploaded a file, it ended up in a sub-directory named manager (the fpdr sub-directory was also created but the file didn't go there). The ID for Manager is 6, and the ID for fpdr is 14. Based on the description for the option, I expected the file to go into the fpdr sub-directory.
This doesn't seem to be the case for users in the Registered group, it appears to happen only to me (because I'm in the Manager group).