Sorry, I was away this weekend so was unable to help with this. Thanks for bringing it to my attention!
It's strange that the popup works for some mods and not others - the input thread is started when the main menu battle begins, so the popup should
always appear regardless of what mod you're using (it just won't work with campaign-level commands until you use addconsole/start a new game). Can you use the console in missions with Exerelin active?
I'll take a look and see if I can figure out what's going on. This mod is going to be rewritten after .6a, so I should probably get re-acclimated with the mod's codebase anyway.
Edit: seems to work normally with Exerelin for me. It's possible it's due to something I've changed in the months since the last release, though. Could you try replacing jars/SFConsole.jar with
this jar and seeing if it works for you then?