Ok here is the update
I found out that the problem is the "quest" plugin.
I don't have many decks and when I started hearthbuddy the program checked for quests. I had a quest where I had to win 2 games with 2 paladin/priest. I have no paladin/priest decks so the program changed my settings in order to complete quests choosing basic decks.
Once the quest is over, tho, the program can't "remember" which settings I choose before and keeps changing deck (no idea about why it keeps changing basic decks tho).
I'm trying to run it for a copule of hours, with no quests and hearthlogger this time, and I'll report what heppens
Ok, even if there are no quests, with the quest plugin, this is what I get on the log after I rebooted HB and hearthstone and changed to custom decks:
[Quest] Now choosing a random basic deck to play with since all quests are done.
So I guess the quest plugin is the problem.
I Hope this helps someone else