I've clean installed every single version of the MacOS since 1.0. I'm an IT geek. :) I know how to get that part right so that is not the issue.
Unfortunately Apple occasionally has problems in their own software (egads, bugs on the Mac OS???) (inserting PCMCIA memory cards in a PowerBook can cause lockups in certain circumstances if the Finder is in the background on a clean system under MacOS X 10.2.6 - old news).
Plus we have to live with Third-Party apps that screw up - Apple doesn't provide everything. Part of the whole point of MacOS X was it was supposed to provide a safe environment to catch those before they took down the rest of the system.
The end result is MacOS X still crashes from time to time. If this crashing is going to produce problems with File Vault then that is a big issue. Losing all your data is scary.
Best to just encrypt by hand what really needs encrypting (not much) and then keep good backups (encrypted or not encrypted as your little heart desires).
By the way, speaking of encryption and backups, be aware that if the vendor who makes the software that you are making backups with stops supporting that software or file format or they go belly up and it is in a proprietary format (even worse encrypted) then you are up the proverbial creek without even a canoe never mind a paddle. Think ShrinkWrap from Aladdin... Much like this File Vault situation.