which graphics card are you using? Maybe it's outdated and time for an upgrade or if not then depending on how old the computer is maybe the power supply isn't outputting as much as it should be and it's effecting the graphics cards ability to properly process high load areas like Defera? Also you might want to manually set your virtual memory to a higher setting then what windows is currently automatically setting it to. As long as you have enough free space to do it upping or even doubling/tripling it might help.
Sorry I can't be of more help but those are the only things I can think of right now.
Oh one other thing, did you recently update the drivers for your graphics card and if you did or if it was done automatically was the performance better before the update?
I play it on an AMD Dual Core 2Ghz laptop with 4GB RAM. I have an ATI Radeon 4200 HD 1GB card. I'm only having problems with extreme framerate drops in the Defera system. Normal gameplay runs smooth most of the time.
I'm glad I found this thread. I've been playing every day for 3 months, and every single time I go to Starfleet Academy the FR drops so bad that even if I turn down everything it's still slow and choppy. Sometimes i can go to a sector and the frame rate is perfect. Game looks crisp and moves very smooth, and other times in other sectors i have to deal with the FR because I just don't have the patience to constantly turn the GFX up and down based on where I'm at.
I had a similar issue with frame rates when ever I went to star fleet academy. I have an nvidia geforce 540m, which isn't the best for gaming. I would never be able to max out the settings unless I was using a lower resolution, or the game would lag quite a bit. This also occured a lot while playing it in 3d mode. I discovered the troubleshooting section, which is on the very bottom of the video tab in options. If you click on the troubleshooting bar, it will give you more options, such as switching your directx, and also adjusting the amount of your video memory limit. I think auto is the default, but the amount of video memory, is small in auto. You have the option of choosing from 128mb up to 1024mb +. When I changed my video memory to 1024mb, which is the amount I have, it made a world of difference. I am able to play it on 1080p, with most of my settings maxed out. I put all of the details to 200%. I also play on very high quality in 3d, and there is very little if any lag.