Can you send me the savegame data for investigation? You'd find them at %appdata%\Running with rifles\savegames\[your campaign name].save. Zip the folder and put it available somewhere or send it to me at
pasi.kainiemi@modulaatio.com.
I tried to reproduce the issue by starting a new campaign and warping to Rattlesnake (can be done by saying /warp 6 in chat in single player). Our faction lost HQ Bravo, died several times there, but we happened to recapture it before the enemy got closer to HQ Alpha. Things worked as expected in this case.
There has been a change in 0.98.4 related to this particular area of the logic which was that if all your spawn points become locked because of the enemy is being close and strong enough to your last remaining base, the timer would continue running in the last base even if the enemy wasn't specifically in the capture zone in order to end the game, unless your last remaining forces manage to push back the enemy before time runs out which is unlikely. Sounds like there could be some issue in there with making the match end properly in such case.
So yea, could be useful to get my hands on the savegame.
Possibly, you can forcibly restart the match by saying /restart or you can change to another map with /warp X. /warp 5 would go to Bootleg Islands, /warp 4 would go to Moorland trenches. You should be able to use the extraction points from there to continue.