So, I am not sure if this will help you or not, but with me, Boxcryptor would never come up. Finally, after just ignoring it for over a year (and a few re-installs and upgrades and such), I got annoyed enough to take a look (and I found your post).
What I found is that Boxcryptor was NOT in the registry to start with Windows!
I just had to add an entry in, and voila, all is good now!
First, if you are comfortable with the registry, go check
and see if you have an entry that points to Boxcryptor. Mine did not.
If you do, I am out of ideas for you. If you do not, then all you need to do is create one.
If you can right click on your Desktop and then select New, then Text Document.
Type in a name for it (I called mine Boxcryptor.reg) making sure that you change the .txt extension to .reg.
Right click on the file you just created and select Edit.
Copy and paste the following lines (if you see two *'s at the beginning and the end, copy everything between them but not the *'s. If you don't see any *'s but you see BOLD txt, only copy the BOLD txt):
**Windows Registry Editor Version 5.00
"Boxcryptor"="C:\Program Files (x86)\Boxcryptor\Boxcryptor.exe"**
Paste the above in the file you just opened and then exit out of it making sure you save it when it asks.
Once you have done this, you can either double click the file or Right click on it and Merge. A pop-up should come up about the Registry, just click Yes. A second pop-up will come up asking about adding information and such, click Yes again. One last pop-up will come up telling you that it was either successful or not (it should be), just click OK.
Reboot your PC and see if it Boxcryptor comes up. Keep in mind, if you uninstall Boxcryptor, this entry will probably not get removed and annoy you or whomever ends up with your PC because it will error when the file is not found. If you run into that, you just need to remove the entry and all will be good, but that is a different file.
Hope this works for you, it did for me!