Here's a fix from another discussion. It worked for me.
Alex G writes:
1. Launch keynote on one device and the remote on the other as you normall would.
2. Find another app that bluetooth links ipad and iphone (I used 'pictransfer light'). Install on both devices and launch on both devices. Follow the promt to get a bluetooth sync.
3. Double push the home button both devices to pull up the multi-tasking and open keynote and keynote remote on the relevant devices.
4. In keynote, go to settings; advances; remote. You should now be able to get the remote to link (you may, on the device running the remote, need to hit settings and then 'new keynote link'.