The changes done in JBIDE-15645 introduced a regression in the way archetypes are selected.
Basically, we can get different archetype versions depending on the EE version of the runtime (web/full-ee6 vs web/full-ee7) but we lost the ability to pick a different archetype version between 2 different runtimes of the same product and same EE level (eg. EAP 6.1 vs EAP 6.2)

As a consequence, archetype versions designed to run on EAP 6.2 will be selected when EAP 6.1 is selected in the project wizard.

Hopefully EAP 6.2 archetypes will still be able to run on EAP 6.1 so that shouldn't be a problem, but we should fix that for the next minor release.