So.... After I tried to plug a conventional generic wired gamepad, steam got crazy and even my mouse started behaving with switched buttons and without scroll while steam was running. The controller worked on big picture mode but not ingame. Then I had the idea of reinstalling steam and wipe out all files and folders inside .steam, except by steamapps.
That solved the problem, both controllers work now.
proton 3.7x1 2019-03
My system information
Dell Laptop
OS: Ubuntu 18.04.2 LTS x86_64
Host: Inspiron 15 7000 Gaming
Kernel: 4.15.0-46-generic
Uptime: 1 day, 3 hours, 37 mins
Packages: 6514 (dpkg), 12 (snap)
Shell: bash 4.4.19
CPU: Intel i7-7700HQ (8) @ 3.800GHz
GPU: Intel Device 591b
GPU: NVIDIA GeForce GTX 1050 Ti Mobile
Running games in a HDD NTFS partition and OS installed on a SSD.
Steam client version (build number or date):

1550534751
Distribution:
Ubuntu 18.04.2 LTS x86_64 4.15.0-46-generic
Opted into Steam client beta?: [Yes/No]
YES
Have you checked for system updates?: [Yes/No]
YES! Up to date
Description:
At about 2 months ago, which was the last time I used this controller on steam, Games such as GTA 5 (using steam's proton 3.7), Mad max and X Plane were detecting my controller and working flawlessly, but I realized it was no longer working yesterday. I always try to keep everything up to date. It is a PS3 bluetooth controller, it is detected by steam and works for controlling the steam's big picture menu. I tried all combinations I under steam's controller configurations, tried reseting the layout, reinstalling the controller firmware but the games don't really detect this controller as it used to be.
I googled for this issue and saw some old issue regarding bad user permissions, so I did the chmod 777/dev/uinput, added my user to the input group, restarted steam and still same problem. Steam itself detects the controller but no response in game.
I could not find anything about controller logs so I don't think they will be really important.
I have a Logitech flight simulator usb joystick and it still works. I couldn't test with a convencional usb gamepad yet, but with this ps3 plugged in usb still didn't work after a steam restart.
Steps for reproducing this issue:
Important notes