Nintendo and famicom have always worked great for me. But I checked yesterday and half of the games I tried wouldn't load and the other half were exhibiting random rapid-fire inputs at the main menus. It did this no matter which controller I used and even if there was no controller attached.
Has anyone else had any issues since the update a few days ago?
I haven't noticed any issues recently but it is probably worth updating your MiSTer.ini to the latest version as there have been some breaking changes if you have not looked at your setup in many months.
Failing that, remap your controllers in the Main menu and check they are in x-input mode if you are using 8bitdo controllers or devices that also have d-input etc. If you're still having problems let us know more about your setup. Which USB hub? Which power supply? Which controllers are you using?
Another cause of mysterious core-specific malfunctions upon updating (especially if you update infrequently, as I do) is changes in the config bits for the core. These generally correspond to changes in the number, order, or defaults of the core-specific configuration options. The framework isn't smart enough to migrate these when changes are made in the core (and I know that seems like a simple problem to solve, but I'm telling you there are engineers who legitimately have nightmares about configuration migration going wrong).
In other words, you might try going right once from the core menu and selecting "Reset settings" before loading a ROM and see if that fixes it. If so, your best bet is probably to then "Save settings" and re-apply any of your personalized tweaks afterward.
If that's too scary, maybe drill into the "Input Options" submenu and see if any of the settings there seem surprising (most of them should be "Disabled"/"Off"/"None"/"No" unless you know why they shouldn't be).