Well , it happens when I create a AAA game and with my R&D Lab is working. I’m getting +30fps with this game normally and then it drops at 1-2fps. I saw that it is because the game with developed in JQuery and it can’t be fixed because it’s a library problem. I don’t think it is my computer either because it can run Skyrim at 30fps easily. It only happens on the 3rd stage of the game , not on the others. If it is not a library problem , can you fix that bug or find a solution ? I’ve a GeForce GT640 and I’m running 1.3.9. If you can , fix that bug as soon as possible, it is (for me) the most critical bug in this game and many many people experience it. It is ruining the pleasure of this game totally.
The Next Update of Game Dev Tycoon 1.3.10 Will Improve the FPS, It will arrive no later than August 2013.
It should help you in this case, and @PatrickKlug He might release a patch or something to improve this for 1.3.9 maybe.
Just keep checking back.
Due to experience, while testing out the TB of 1.3.9
Are they Test Builds ? If I can have one of these maybe it will solve the problem even it is buggy a little bit , doesn’t matter for me too much 
Send an email to our support quoting your order number and we’ll send you a test build. We’re still unsure what exactly causes this as the hardware for most users seems to be powerful enough.
The next update which is estimated to come out in August 2013 will also include some improvements to FPS.
Yep, I’m also having this problem! I find restoring/maximizing the window helps it temporarily. I sent an e-mail to support for the test build, hope I get that soon !