I just came to report this as well. I just checked and it also happens for me in F&R. As a test, I started a new scenario. I looked in the saved game folder and noted the timestamp for the initial saved game file. I went back into the game, plotted some moves, advanced a turn, and then saved again using the same file name. After the game resumed after saving, I checked the file folder. The timestamp was still from the original. As expected, when I closed out the scenario and reloaded, it was the earlier file.
I know this is new behavior because saving over the top of previous saved files has been my standard procedure since Shock Force 1.
EDIT: Sorry, I now see there was already another thread on this issue.