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robot_pose_ekf can work just fine with gmapping. Watching your bag playback it just looks like gmapping is having trouble converging. If you watch in the /odom frame everything looks pretty solid. With 10 seconds of decay on the laser scans they seem to blur ~ 10cm which is good.
You're driving through a very repetitive environment it's not too surprising that gmapping is updating it's estimates frequently while you're still exploring. You may also want to close some smaller loops and incrementally build up your map to help gmapping build up confidence incrementally. And tuning gmapping's parameters to make sure to match your robot is important.
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