Strange, I've just started having exactly the same problem today. I just assumed it was because I unloaded then loaded the mods through JSGME (to try to fix the CO2 bug which I hence succeeded in). I can't load up my out of port saves and now after restarting from last port save and spending a few weeks out on patrol loading the save eliminates the terrible weather there was, but also the merchant I was on my final approach towards.
Haven't been able to find any info about this anywhere else, so hopefully there's a fix.. I was about 8 submissions into my patrol when the savebug occured.
P.S. I'm -not- using the steam version and I am also using TMO 1.8b+RSRD, so that rules out that being the cause.