Are you using send to compressor or are you exporting a reference movie?
If you are using the export with compressor option, my research suggest simply don’t. It ties up FCP and you have two progs running needlessly.
I always use reference movies. When exporting use the Export to Quicktime, then make sure your settings say current settings in the drop down and that audio and video is selected from the second drop down (you can do video only or audio only as well).
Lastly (this is the important bit) make sure that the box that says make self contained is UNCHECKED save that to your project folder or where ever you have your FCP footage stored (just being tidy here). Then import that ref movie into compressor and apply your settings as you normally would. You can then close final cut after you have exported the ref movie. So hopefully no final cut is open to crash, this might work for you.
Also if you have a load of sequences that need editing you can carry on working in final cut as you normally would whilst your movie exports as the reference movie does not use final cut at all. The reference movie only points to where your footage is, so make sure all your elements are online e.g your external is on.
Personally I have one folder for each project and anything and everything goes in that folder. None of the elements for my movies are on the desktop or in some folder on the comps HDD its all in a project folder on the external. Oh the joy of data management.
Sorry for the waffle hope that all helps.