I am using the git 1.8 stable repos, though my site is reporting 1.8.2Testing. I did a git pull on the site tonight and it prompted an upgrade. On performing the upgrade it stuck with various error messages (I didn't screen shot as I wanted to fix it, but it was errors in /lib/db/upgrade.php; /lib/dml.php; /lib/ddl.php; /admin/upgrade.php and /admin/upgrade.json.php) . The messages related to a modification of the usr_custom_layout table. In the upgrade xml it was reporting to add to the existing table. The old version had, as far as I can tell, no group and institution settings. The new table xml says to build into the table the group and institution tables and the corresponding foreign keys to link these tables. I am no developer, so this was more brute force and ignorance, but looking at various files I can see that the only foreign keys required are the user table and view_layout. I used phpmyadmin to delete the other foreign keys and linked the fields in usr_custom_layout to the corresponding id fields in user and layout_view and the update completed.
Apologies as I went around in circles a bit between work and it is late on Friday so well into beer time.
Hope this makes sense.
Do you have the problem also with 1.9, the currently latest Mahara?