Yesterday, I experienced a slowdown of the fps in-game (on the Galactic and tactical maps), then the Save and Quit functions slowed down significantly (~1 minute for each to open and activate). Changed from disk version of SWFoC to Steam, plus performed numerous scans (Norton, CCleaner, Scandisk, Malwarebytes, MS Defender, etc) - no problems. Using the Steam version, an ICW 2.1 save started Ok and rapidly slowed down until saving a game and quitting that campaign took minutes.
Tried again today - same thing only this time: Quit game stopped working, Cntrl-Alt-Delete was extremely slow to open, CPU usage and memory usage shot up, and SWFoC stopped responding.
Update 9-15-17: after two+ weeks of searching/testing for a software/OS/virus/malware/HD/etc problem, I took my PC/mini into the local computer geeks and eventually learned that a liquid cooling hose had a kink in it that over time caused the pump performance to deteriorate resulting in very high cpu core temperatures. Installed air cooling and fixed the problem.