I've just manually upgraded a couple of per user plugins and its not recognising that I've upgraded them. For example I upgraded the Calendar plugin to 1.2.2 and this is the text version of what I see on my plugin screen:
Calendar
This plugin allows you to display a calendar of all your events and appointments as a page on your site.
Deactivate
Version 1.2.2 | By Kieran O'Shea | Visit plugin site
↑ Activate Calendar Site Wide
There is a new version of Calendar available. View version 1.2.2 Details or upgrade automatically.