(** I have an iPhone btw **)
I had the same issue and filed a ticket with Runkeeper. They replied telling me that while they don't have knowledge of such bugs, they'll keep an eye out. I think it'd be nice if you could file a ticket to let them know as well.
I found a 'workaround' that seemed to work for me so far.
1. Make sure you keep Runkeeper running in the foreground. Somehow keeping Runkeeper in the background while the screen is locked may be doing something to the connection - not sure why or if this is the case, but it's worked for me so far.
2. If you need to head indoors where you can't get GPS for longer than a couple minutes, pause or better yet, just stop the exercise. I've had mixed results with this one. I've had situations where my Pebble was able to re-establish connection after extended paused indoor sessions, and where either the Pebbled showed 0:00 or just a frozen screen.
I've done the two steps above and I have yet to have a single freezing or hiccup so far. The workaround is counterintuitive, yes, but deviation away from those two have resulted in either freezing or resetting of the Runkeeper app on my Pebble.
*P.S. Even after the Pebble freezes, Runkeeper app on my iPhone continues to run just fine. I've had cases where I didn't want to pause/stop an exercise just for the Pebble so just finished the session without.