I have 32GB of RAM, disabled page file (as you suggested, but did it long before I read that), and I have the exact same problem. Game runs perfectly fine for about 5-10 minutes or so, and then every few seconds it freezes for 10-12 seconds, and if this continues long enough, the game just completely freezes up. Running an i5 3570K (no OC), and a GTX 460 SE (no OC). More than enough system to handle this game, I've been able to run every game before this perfectly fine. Without the trainer, game works perfectly fine as well. I've never run into this problem with your trainers, and I've been using them for many years now.
ran trainer ran game press F1 at main menu started single player game with 4 AI moved ships around for 2 minutes no freezing added credits and minerals moved ships around for 2 more minutes no freezing used hull options used fleet supply used capital ships used tactical slots did some instant research built some ships moved multiple ships around for 2 more minutes no freezing did some planet upgrades moved around ships for 2 more minutes no freezing.
10 minutes wasted. trainer working fine here with no freezes.