I also found that we had this issue today.
Upgraded from 2.2 to 2.7. Mostly seemed to be working but same error:
"Table assignment _upgrade does not exist"
On looking around, within the mod/ folder, Assignment was not there although seemed to be in the zip file of the moodle version that I installed.
I installed Assignment (zipped from the 2.7 moodle and uploaded just that folder) , which did install the table and the automatic upgrade started. The majority of the rest of the assignments went through without any hassle after that using the up-grader.
It appears that although it seems like was in the 2.7 zip file, something deleted it before it ran an upgrade and thus no table was created for that function to run. I am baffled as to how/when it was removed. Adding it back into a 2.7 moodle allowed the table to be setup (saw this in the Assignment setup xml file). I guess I could remove it again now it has all gone through.