hey, sounds crazy that it would work after shutting AE down and then on again. and again that’s not an entirely fun thing to do all the time. I actually had the same problem and what I had to do was to check the settings in Illustrator in > preferences > file handling & clipboard :: and there check that it copy to PDF is not checked and that AICB is checked together with preserve paths. after I sorted that it worked a charm. you might have done this already and have another hitch on the line somewhere, but it might be worth a look.
good luck
/d 🙂