I can get laggy FMB and also missions simply by installing more planes, so that is one thing to test. In UP2.01 with Q6600 CPU @ 2.4 GHz I got clearly laggy FMB before Java memory crashes started, and even with current DBW and i7 2600K @ 4.2 GHz I can get quite bad lag with all possible planes installed, but I need a new beta selector that should be included in DBW 1.7 to avoid crashing. I have nVidia GPU in both systems, but I think that plane number lag is on the CPU and Java side and thus GPU doesn't matter there.
Anyway, it is useful to test with less planes active in air.ini and if it doesn't have any effect, then you have some other issue there.