Are you using gcc?
Then this one for sure will help:
Reducing the build time with gcc for ARM and CodeWarrior | MCU on Eclipse
I don't think another Eclipse is a problem. I'm using Windows7 64bit and running 2-3 Eclipse instances many times.
What else helps if you could close projects in the workspace which you do not need right now. Having many projects open at the same time slows down Eclipse, but not sure if this is the case here.
Another thing is Cygwin? Do you have Cygwin (c:\cygwin) installed on your machine? I had issues in the past where the GNU make somehow was searching and using the Cygwin make. If you have cygwin installed, you might try renaming that folder temporarily to see if it has an impact.
But still, these kind of things would not add over time. I understand that you say that after you close Eclipse and start it again, then things are ok again, but then degrade over time?