I see that this problem has been addressed before, but not in the past month or so I think. I have the issue where I login and go to the Updates->WPMU DEV area and my API key is all angsty and red. I click on the 'Update Now' link or the 'Check Key' button and it changes to a nice, calm green. However, if I straight away (or any time later for that matter) click on the Updates->WPMU DEV menu it immediately goes red again.
So, it seems that the key is fine but something in there has a serious short term memory problem. I've attached 3 screenshots.
1. Logged in and went to the Updates->WPMU DEV area. No updates listed and a red API key.
2. Clicked on the 'Check Key' button.
3. Repeated step 1.
The numbered screenshot files correspond to the steps.
I also noticed this time (having not logged in for 5 or 6 days) that the key had been removed from the Anti-Splog settings and there was a message when I logged in telling me that I didn't have an API Key set for Anti-Splog.
The domain is correct and the key works – but only immediately after I update or 'Check Key'. I have Anti-Splog v1.1 and Update Notifications v2.1.