That something else can be EuroScope or any loaded plugin. Re-setting the already set "CA" assigned altitude (1ft) would clear the CAT2/3 flag even if the value remains the same as before - the plugin considers this as a change to a normal "CA" assignment, and based on the limited information available here it would seem as the most likely reason for the disappearance of the CAT2/3 flag.
Assuming this is correct, it should be possible to fix it by keeping the CAT2/3 flag when the cleared level is not changed - the "CA" item in the CFL menu would then be changed to specifically remove the flag. The downside would be that other plugins would then no longer be able to "downgrade" the clearance just by setting "CA", they'd need to first set another cleared level and then "CA" again.
