You certainly are getting short of HDD space and that can cause some quirkiness. Although you are using an external, there is probably reading/writing as part of virtual memory used by the apps. If you can free up some disc space, that's always a good thing. Anyway, make sure you are using the Subler beta and if you are using a HB nightly build, go to the approved version (0.9.6) and see if you application stability improves. Also, sometimes just a reinstall will improve things. If trying a different version and/or reinstall of HB does not solve the problem, I would recommend going to the HB forum and provide the activity log. They can pinpoint problems from that and give more technical help that will be hard to find on this forum.
I had the exact same issue you are describing when I was using the "non" beta release. Lot's of crashing and usually when selecting/importing metadata. The beta version has been rock solid. As for HB, I have had an occasional crash but they are very rare. I do not use the queue, though and if you do, it might have something to do with that.