I'm still chugging along with an ancient Dell XPS 400, Win XP media center (kind of half assed XP pro with a movie maker app) upgraded a few times with a Pentium D 3.4, 2 gigs RAM, Nvidia GTX 650 2 gig, and a SSD. Running SH4 off the F drive (the SSD) I get better performance than 12 years ago, but if the patrol runs on long enough and I get 300,000+ tons (happens a lot since I have all these resupply bases) it will sTTTTTTart sTsTsTuTTTTTering in TTTTTTTime compression.
Only cure I've found is quit before it gets up to 400 thousand, return to base, end patrol, start a new patrol and the stuttering is gone. Until I go crazy again, of course. Not really an issue if I don't get carried away, medals max out before 200 thousand tons anyway, and by the second patrol I have more renown than I can possibly spend.
Get back to base, end patrol, see if it does it after starting the next patrol - save files getting fat is my main theory, although I haven't proved it yet.