Unfortunately, I don't know of any fixes, but it's a confirmed issue that I've had when running multi-refit patrols. The game seems to save quite a bit of information as time goes on, but it doesn't dump out nearly as much, if any at all, of the old data as the new data comes in. As the campaign tries to keep track of more and more enemy ships, events, and the like, it just gets to be way too many calculations for the CPU to handle, even with high-clock multicore processors. Sad truth is that the game engine just plain isn't equipped to handle the immense number-crunching required for high time compression with that many contacts to monitor.
As a side note, it does make sense that aggressively high TC settings will appear to run slower than moderate ones; you're asking the processor to execute 5000 commands per tick instead of 64 commands per tick, which certainly doesn't help matters any when it comes to an already bogged-down data stream.
Sorry that I can't help you for this particular patrol, but in future patrols, try and hold them to a somewhat moderate length. If you're based in Pearl, factoring in travel time probably means you can only afford one refit, two at best, before you should start thinking about drydock. I've been able to get away with three or (very rarely) four refits when I'm with my Asiatic flotilla, but even then I can notice it starting to chug along a bit. Ultimately, also bear in mind that "refits" isn't really the best measurement of time to gauge a patrol, since it can vary pretty widely; but, having said that, it's still the rule-of-thumb I usually abide by to help keep the pipes clean when I'm heading home. Perhaps someone else can give you a more solid estimate, but I think individual results will still vary when it comes to how long a patrol you can get away with, based on hardware capabilities and the amount of random data the engine throws at you unless you're running one of the static campaigns like RSRD.
The bad news? I figure you can either cut your losses, load an earlier save, and make for home base at a fairly good clip, or you can just stick it out and putt-putt your way back home. At any rate, hope this at least helps ya a bit even if it wasn't exactly what you wanted to hear.
