Substitution Levels are being imported into the Character (into the classFacet) without having their Qualified Key (which is used for the source for terms) set.
This results in CL being tested against the substitution class name (e.g. "Super Fighter") rather than the base class name "Fighter". Thus CL returns zero.
See https://groups.yahoo.com/neo/groups/PCGenListFileHelp/conversations/messages/24454 for the original thread.
Committed revision 23071.
I take it this is good to put in 6.2.1?
Yes this one is fine to be included in 6.2
Backport to 6.2: Committed revision 23091.