Welcome to this forum. Please provide more information about your setup:

all the information that's asked for in https://retropie.org.uk/forum/topic/3/read-this-first What do you mean by "not the same"? Are the control settings different or gone? Does the effect happen in Emulation Station (the frontend where you choose the games) and/or in the games themselves? What kind of "a few things" did you try?

edit: typo