And if it does turn out to be a bigger issue and won't update you could try doing a clean install and then just copying your new exe files into your old build. I would suggest either renaming or backing up your old exe files in case it doesn't work though just to be safe.
Next Wednesday MAME 0.199 comes out so you may just want to wait a few days until then to download the roms but totally up to you. Onto the images LB is only downloading what you tell it to and since it was changed to support more than one cover image due to people insisting on that feature to accommodate games with different covers from different regions that is just something that happens unfortunately. How did LB delete your Arcade games by the way as I see you've said that in the last few post and did you check the backup folder to see if there was a copy of your Arcade.xml to restore them from.
I just use Torrent check to update mine it does require a little manual work but I find it to be very simple to use it its located here on the PleasureDome forums
http://forum.pleasuredome.org.uk/index.php?showtopic=26754
well say if you still wanted to use your control for it you could actually edit the code to be alt+f4 instead of escape but if removing it does the job for you than glad you got it all sorted out
If you are using LB controller automation and it uses escape in the emulator the ahk that can easily be edited to use alt+f4 instead because there certainly is a few stand alone emulators that use escape in that manner.
I'm not really sure but the fact that it dictates where your chd files go and will either move them if you let it or list them missing if they aren't in the folder is one of the reasons that using the program wasn't for me.
Not sure then if it was MAME I had some ideas of what it could be and if I'm reading your original post correctly some of the games in the platform are working so it sounds like it is configured correctly.
I would suggest next Wednesday when MAME 0.199 comes out you head over to Pleasuredome.uk.org and get the latest set and the same with going to the official MAME site and getting the latest emulator then at least you will know what you have for next time you may decide to update your roms (if you ever decide to)
MAME releases new roms every month and they will be doing so again in 5 days on Wednesday of next week. Sometimes ROMs that are already in MAME will get revised as either new dumps will come out are a new version is picked to be the parent leaving them to change the name of the old parent to reflect its a different version its all a little complicated at times but things can change and that will break ROMs from time to time. As Neil mentioned some time ago now all Capcom CPS 2 ROMs added a qsound file to it so any versions older than those revisions certainly won't work any longer in MAME.
In RetroArch there are a few different MAME cores depending on what roms you have will determine which version of the core you want to use.
SNES9x is fine but Higans and BSNES are cycle accurate to the SNES so they are technically better.
Model 3 and Model 2 are not emulated in RA at this time.
Some of the best cores for certain systems are
Higans or BSNES accuracy SNES
Mesen NES
SameBoy GB and GBC
Sega Genesis Plus GX which is every thing Sega before 32X (32x will require Picodrive core)
MAME will depend on your ROMset
a lot of the other stuff only has one core so hope that helps if you have any specific questions about any system just ask for ones I may have left out.
Something is not normal there shouldn't really be any difference between your keyboard and your controller in this regard. I have all xinput controllers and don't have this issue either.