Sometimes roms can come back with multiple possibilities while being scraped. Scrapers like Skyscraper for example, will usually pick what it thinks is the best match. I believe you can use scrape by checksum to ensure scraping accuracy.
You can always delete the gamelist.xml and re-scrape your roms.
There isn't any such software, I guess you just choose to ignore the advices in the other topic telling you to follow the Arcade quick start and not try to 'find the emulator for the ROM'.
The only software that can decide if the ROMset is valid for an emulator is a something like CLRMamePro or RomCenter - or some other ROM audit tool.
Well i got round to testing that as it was sat on my pi anyway i can confirm contra 4 works fine i have a us dump if its relavent and if i may suggest you could try checking your controller mappings see if shoot and hook isnt mapped to the same button by mistake you never know may have overlooked it but it is working fine infact ive just been playing it with my ps3 controller on my pi with enhanced resolution enabled(actually gives 2d games a nice crisp appearance instead of the default blurred one)
In general I am missing more display options, like what I have in Mamextras on my Xbox already: I want to filter only 2 player games, or only 4 player games, only clones, only parents, only fighting games, only games starting with a, etc...
EmulationStation does support filtering by the metadata so you can filter by player count or genre. However, clone/parent status is not part of the metadata that ES is aware of so you cannot filter on those. The filter options are available in the menu when you press 'select'.
The /opt/retropie/configs/all/emulationstation is actually the same folder as /home/pi/.emulationstation, the latter being a symlink to the former.
Emulationstation reads the custom file in /home/pi/.emulationstation, then - if the 1st doesn't exist - the default one /etc/emulationstation/es_systems.cfg (installed and maintained by the RetroPie setup script).
I never got any upgrade to ever write a custom ES systems file in that folder, but I'm only using RetroPie since 4.2.0 - so it might have been a problem in the past.