@hansolo77 Thanks.
You may have a file named /opt/retropie/configs/all/retroarch-joypads/MayflashLtdMayflashMDUSBAdapter.cfg or something. AFAIK, RetroArch will get the configs from this file no matter if you have a MegaDrive or an Atari 2600 controller plugged. It can be annoying.
When you want to come back to this issue, my suggestion is to hardcode the mappings for atari2600 in the file /opt/retropie/configs/atari2600/retroarch.cfg (you may want to have a keyboard plugged in order to solve the issues you mentioned for start button, etc.). You can get the instructions on how to edit it on the wiki: https://github.com/RetroPie/RetroPie-Setup/wiki/RetroArch-Configuration#hardcoded-configurations