I will admit my mod list is....full.
I have all of the SS+ supported factions plus SCY which is unsupported (culprit?). The crusade was occurring in Gigas, with 1 Shadowyards heavy fleet, 1 Hegemony Heavy fleet, 1 heavy Templar fleet and 2 small Templar fleets plus my own (5 ships including a newly-captured Crusader).
I have never ever had any issues with StarSector with 4gb allocated (even back in the days of 20 races). Even now, with SS+, 0.65.1a, and my current mod setup, the game would never go beyond 3 gb of usage, with an average of 1.6 gb, up until that save at least.
Personally I just don't understand it. Guess its time to start a new game.

Edit: I can see about uploading the save itself if it would help. I actually took a look at it in Notepad++ and the save file itself is a whopping
122 megabytes! It even lagged Notepad++. My average unzipped save file size is 84 megabytes even at level 40, so I have no clue what happened.