It must have been something to do with the configs from the previous version getting in the way.
I did as you said and access the Mod tab in the Configuration menu, and there were the three mods, disabled. I enabled them, and then the game style changed to the one I got used to from the previous version, and hitting Play would take me to the screen to chose a slot.
There, the first slot was occupied. Then was when I realized I had still the previous settings. Sadly, the game overwrote the mods.txt settings file when I enabled the mods, so I guess I cannot recover the old content to check what the hell was in it not to let the game start.
Thanks a lot for all the support. Now time to play! :D
[gallaecio@afonsox flare-git]$ sudo pacman -Ql flare-git | grep mods.txt
[gallaecio@afonsox flare-git]$ cat /usr/share/games/flare/mods/mods.txt
# Mods lower on the list will overwrite data in the entries higher on the list
[gallaecio@afonsox flare-git]$ /usr/games/flare
Unable to open engine/tileset_config.txt! Defaulting to 64x32 isometric tiles.
Unable to open engine/misc.txt!
Unable to open engine/combat.txt!
Unable to open engine/elements.txt!
No joysticks were found.
Using joystick #0.
Mix_LoadMUS: Couldn't open '/usr/share/games/flare/music/title_theme.ogg'
I cannot but think of Matrix looking at this tileset.