Here a few things you might try:
1) Start the NeoLemmix.exe, go to Options -> Hotkeys and make sure to uncheck the box "Show unassigned keys". Now you should get a list of all hotkeys and their corresponding functions. Are the correct hotkeys displayed there?
2) Attach the file NeoLemmixHotkeys.ini here, so that we may have a look at it. In this file, all hotkeys are stored.
3) Move the current NeoLemmixHotkeys.ini in another directory and start NeoLemmix again. It should now create a new NeoLemmixHotkeys.ini with the default hotkeys. This way you can at least use the default layout again. Disadvantage: If you use a custom layout, you have to reassign all hotkeys.
EDIT: No need to delete the NeoLemmixSettings.ini, if it is just the hotkeys and all other options are working fine.