I've noticed this issue in the past when converting AP's. It seems like my Master 4404 will take some AP's that are converted with an SCC and allow them to connect. However, some it does not? My standby controller with the allow SCC option turned on as well, allows any to SCC AP to connect? What gives... Also, it's a little confusing since the upgrade tools says you need to import the files, but you apparently don't except in some cases? By the way, I haven't tried importing the files for the AP's, and that would probably work.. but why doesn't the Allow SCC option simply work? Or why does it work for some and not others? I'm using c1200/c1230's and c1130AG's.
This isn't an exact science as you have seen. We did experience some problems when we did these conversions as well but eventually got them all done :) Are you using the latest version of the Upgrade Tool? Can you use the Controller that seems to work better as the Master for these conversions? Have you tried upgrading less than six at a time?
Here are some docs that helped us for sure;
Self-Signed Certificate Manual Addition to the Controller for LWAPP-Converted APs
LWAPP Upgrade Tool Troubleshoot Tips
Hope this helps! And best of luck,