Hello Cody,
It's difficult to be sure what the issue is from your description but you could try the following.
Stop Trimble Sync Manager (including exit from the System Tray)
Rename the C:\Users\<user>\AppData\Local\Trimble\Trimble Sync Manager\ directory to something else Trimble Sync Manager_OLD\
Restart Trimble Sync Manager
(You may need to start Sync Manager twice to get the sign in screen to show)
During this process, Trimble Sync Manager will create a new local cache of data so all of your existing cloud projects will need to be re downloaded
TSM local settings such as periodic downloads or proxy servers will need to be recreated
If this doesn't clear the issue you may be better off reporting this as a support issue through your supplier.
Provide the C:\Users\<user>\AppData\Local\Trimble\Trimble Sync Manager\tracelog.txt
Regards
Chay