You might try the extract command instead.

The seperate command will seperate distinct sections of geometry that are not merged together, but are combined together. For example, if you made two spheres and jammed them together without vert-by-vert merging them and then combined them, they'd seperate back into 2 objects with this command.

Extract will take faces out of a piece of geometry even if they are merged.

Can't say I can help with the crash bug... sounds like faulty software.