I used a fresh installation on the latest build on January 4 this year, I guess it was 3.x, can’t check now.
Now I grabbed the latest version for the RP2. Could they really have changed that much in this little time? Or perhaps the RP1 and RP2 emulators differ?
When I had to reinstall RetroPie I noticed that some game systems were configured to use different emulators than in my old configuration. Realize that there often is more than one emulator to choose from when running a ROM. To choose: move the D-pad (or any key) a lot during start-up of the emulator. A configuration screen should pop up where you can set a different emulator for the type of ROM.