Put your Vita in Airplane Mode, then power it completely off. It is likely still recalling the last prompt in its RAM telling the console that an update is available, but the system is not up-to-date.
Make sure you are using the most current version of Content Manager Assistant. If you're not sure, go to Wololo.net and grab the latest Open CMA, then completely uninstall CMA from your system, and delete the folders.
Then, reinstall the updated official CMA, crack it with Open CMA, turn your Vita on, plug it in and go to Content Manager Assistant on your Vita, and it should work.
I did this not even a week ago with a brand-new PS Vita that had 3.01 out of the box. I was able to activate it and everything. Let me know if you run into any problems.