Yeah, sounds like you're confusing Repeater with Key Maps. If you share your config it'd be much easier to see what's wrong with it for your first issue -- unless the issue is that you have Key Maps off and Repeater on, in which case turn Key Maps on. To do so, select "Copy ISBoxer Toolkit Profile to Clipboard" from the File menu in ISBoxer (you'll get a privacy box if you want to keep character names private;account name is censored by default), then go to pastebin.com, paste it there, and then link to it.

For your 2nd issue, the option you need is in each Slot in your Character Set. You can set it to broadcast F1 when you press F1, F2 when you press F2, etc.