I know this is a 2 month old thread but I am experiencing EXACTLY the same issues
However I just purchased Fences 3 so Folder Portal navigation has never worked. However, I loaded another users Windows account and it works.
I just need to figure out what is causing the conflict.
I have directory opus (but have temporarily uninstalled it - navigation still doesn't work. Strangely when I did have DO installed if the Navigate folders is turned off double-clicking on a folder will launch DO - which it is setup to intercept Explorer calls. But when navigation is on the same action opens up Explorer - which is a little strange)
I have also turned off Dropbox, Googledrive, Onedrive and Kaspersky to no avail.
I wish there is away to figure out what is happening. The Folder Portal navigation looks awesome!