Sorry, but your post here is extremely cryptic (at least IMHO). Certain things need clarification.
So you boot up with these external hard drives already plugged in to the computer, and they mount and Caja reads them just fine?
So you connect another external hard drive; it automounts properly; but when Caja goes to open the newly-mounted disk, a new Caja window opens up, freezes, and then all Caja windows disappear?
Pardon my apparent attitude, but what makes you think Caja doesn't crash when all Caja windows are closed spontaneously, never to open again by themselves?
If you're even thinking about this possibility right now, it's a sign that you should enumerate how many devices you actually need attached at one time. Computers do all kinds of wacky things when you deprive them of juust enough power. Even if...
That might give it a little bit of a break, but from what you're telling me you've got devices attached like nobody's business.
Side note: With all these hard drives here and hard drives there, that's yet another data point for my thread: How much space on your storage devices do you really use or need?
That's not a given, but admittedly it's less likely that they'll be GPT than MBR.
It most definitely is.
Did you ever click "Ignore future crashes of this program version" in any of the dialogs? Did the dialogs regard Skype? Also, if the dialog actually said "Ubuntu has encountered an internal error", then that probably refers to a desktop component like Caja, and not some third-party application like Skype. If the dialog said "The application Skype has closed unexpectedly", then that would indicate a Skype issue.
For starters, reproduce this bug by plugging in a drive while the system's running, then execute at the terminal:
grep -i caja ~/.xsession-errors
Paste the output of that command into a post here, select the pasted stuff, and click the </> at the top of the post editor. This can help us figure out what's wrong.