Hello,
Presently, my pop 3 accounts are set to open in Thunderbird and were working. Very recently, not sure when, Thunderbird won't open when I click the account. In options, for the accounts, I checked and the path is correct.
Firefox (43.0.4)
Windows 10 (Threshold 2, Fall Update, build 10586)
Thunderbird (38.5.1)
Working for me
I have Windows 10 (version 1511, build 10586.29), FF 43.0.4, Tbird 38.5.1... and clicking my POP3 account with the Link defined to open Thunderbird worked for me.
Are you clicking your POP3 account in X-Notifier's drop-down account list (right-click the X-Notifier icon envelope)?
I set my Link in my POP3 account properties to...
file:///C:\Program%20Files%20(x86)\Mozilla%20Thunderbird\thunderbird.exe
...(it apparently doesn't matter whether you use forward slash or backslash, in the program path for the Link specification... but it does for the "file:///", I think).
Note the (x86) on 'Program Files (x86)' in the path.