It's not only RetroPie that changed over the years, but also prboom. There's now a core option for the FPS (I think the original Doom ran at 30 or 35FPS), check if yours is set to 60 FPS.
Also, when opening a help topic, please add more info about your system and setup, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.