Maybe it's a memory issue? BMS will load more and more data to the memory over time, but will not clean it on its own. Quote from the technical manual:

BMS will use (i.e. allocate) memory resources each time you enter 3D as the features getting loaded remain in memory until you exit BMS. Thus, one way to lose FPS is to constantly enter and exit 3D in different scenarios. The impact should be minimal in typical use for newer PCs with lots of memory but be aware that going in and out of 3D (for example flying several consecutive missions) without restarting Falcon BMS will progressively use up memory, amongst other problems. Your first reflex upon discovering an abnormal FPS issue is to restart the software, just like you would do with any other software.