This is a know issue with upload to RunKeeper for activities without GPS data. CopyMySports is providing all heart rate data of these activities to RunKeeper, but RunKeeper is not including the heart rate data on their site if the activity does not contain GPS details. We have reported this to RunKeeper more than once and other developers are experiencing the same issue. Unfortunately it is not yet resolved.
CopyMySports cannot resolve this since it is already providing the heart rate details to RunKeeper, it must be solved on RunKeeper side.