Gotta love Harem, holding onto those manually created commands instead of using ISBoxer p.s. try not to confuse people by posting them :P

My problem is that after intense BG PvP fighting, i'm left with a repeater state hanging around,that toggles whenever I swap to another character.

If I use my Toggle Keyboard and Mouse (Tab) Key ,(in my main window), to get rid of it,then shift to activate another window,it comes back and I have to toggle it away again.
The Repeater state is per window. If you want it applied to all windows when you hit a key, you need to make sure that your hotkey is changing it for all windows instead of only the current window. Personally I only apply the repeater state to my current window, but clearly in your case you want it applied to all. If you have a key that toggles one, and a key that toggles all, then you need to be careful about which you use.

For Jump/fly up, you need to make sure Hold is enabled for that key, like Nolife mentioned (which will roughly translate into what Harem posted, but dont let him confuse you, you don't need to know what it's doing behind the scenes)

If you continue to have problems, please share your ISBoxer config so that I, or anyone else looking at it, can give you informed suggestions. To do so, right click on "ISBoxer" at the top in the software, click on "Copy ISBoxer Toolkit Profile to Clipboard", then paste it wherever -- here, in email to me at lax@lavishsoft.com, in the ISBoxer Chat room, etc. Whoever looks at it can then copy and paste it into ISBoxer to see what you're doing (or if they are masochistic they will read the XML).