Unfortunately that did not help, tried it a couple of times she is still the only character (at least on the stats sheet) who misses the entire section of weapon proficiencies.
I did some further testing and I think I found that we need an extra step if we want to repair it in a running game (This would not be required for Imoen joining in a normal way with the current mod's version.)
It looks like the proficiency menu is only updated on certain events (Joining party, level up, maybe others).
1. Put this file CVIMOD.SPL 346bytes 2 downloads into BG2EE/override
2. Make sure you have this block of code in your Imoen_,BCS
3. Kick Imoen out of the party but keep her in sight!!!
4. Via console do C:SetGlobal("profs","LOCALS",0) you must have your cursor over Imoen when doing the input
5. Let her rejoin and check the result.
I tested it with mage Imoen and mage/thief Imoen and it works for me.