This is an easy one
If you export a SAINT template of file it is currently using version 2.0 but this version is not classifying keys that have commas in them
Please make the latest SAINT template (2.1 as far as I know) the default for all exports
It's really amazing how long this has gone on. (And how annoying it is to deal with.) This is one of those cases where the problem should be considered a bug, not an "idea".