Are your ipad and ipod running different versions?
I did a bit of googling and it seems that iOS5 broke the bluetooth part of keynote remote but then 5.1 fixed it again. I don't know if you have to have the same versions of iOS on both devices but would hazard a guess that you do.
Sorry if it sounds like Grandmother sucking eggs etc but I did have a bluetooth connectivity issue between my ipad 2 and iphone 3G after upgrading the ipad to iOS5. I fixed it in the end but it took lots of messing around.
Let me know if you want the full SP on what I had to do