For those who would encounter the same issue...
My pc being out of order so far, I reused an old laptop running vista (I know I know...).
I installed ET on it, pasted my main folders and files, set run as admin everywhere it was needed. All seemed ok.
Connected on NQ server, went fine.
Tried to connect on Jay2 and everytime I had this message kicking me of the server : "Couldn't reopen Enemy Territory\etmain\pak0.pk3".
I googled and FAforumed on this but nothing really serious. Updated the drivers. No change.
Then compared NQ and JAYMOD folders, and saw that it was a all mess of old .pk3 files. Manually removed alot of them, mostly related to old servers I used to play on and it works fine now.
Good to try.