I had that issue myself. I ended up taking a SQL backup (I make them in 6 hour intervals) from a 6.1.4 version and then dropped my tables, reuploaded the upgrade packed, reimported my latest backup and since then, no Ads. I don't know if there was an issue with the license server or not, but so far, (knock on wood), it is running ad free once again.
You may want to try that. OR, if you have not made many mods to your site, backup your tables, drop them, nuke your site, reinstall from the full package, reimport your tables. I did that on a test server. Funny thing happened there, it removed ads until I logged into admin and told it I didn't want to license since it is domain locked. ;) Once I went back to test server, it showed the boonex ads.
Best to do this when your site is not active of course, so that may mean working at 2am.