If the iPhone's screen is locked, the watch will stop tracking. However, the iPhone app will continue to track, and when the iPhone's screen is unlocked, the watch will catch up to the iPhone's tracking. This problem also seems to occur when the Runkeeper app is in the background as well.
This issue is currently affecting newer, updated Pebble devices, such as the Pebble 2 and Pebble Time Round. If the Runkeeper app remains in the foreground of your iPhone's screen, both devices should track in tandem correctly. That seems to be the only workaround at this time.
However, Pebble has recently shut down operations, and won't be able to improve upon the functionality of their last update, which makes it difficult for us to continue implementing fixes related to the integration. This means existing bugs like the one you're experiencing, will remain in place for as long as we still support the integration.
We're sorry about the news, and wish there was more we could do! For further context on Pebble's situation, check out their latest blog post here on Pebble's site.