Wow, that's a big difference.
It couldn't hurt to go back and recalibrate the ESCs, especially the port one. The calibration sets the incoming pulse-width range to 1000-2000 usec, while I believe they come from the factory set for a somewhat wider range. So perhaps the port thruster lost its calibration, and is running at a lower power than what you are commanding it to be.
If you have a programming box for the ESCs it couldn't hurt to check that they are still programmed correctly. Several people have had issues with the ESCs forgetting their programming, though I don't think that's an issue here. BTW, on the new OpenROV 2.7 announced today, we've ditched the old ESCs altogether and have gone with a version that is programmed via the controller board's arduino. The controller board will come from the factory with the ESCs pre-installed, pre-programmed, and pre-calibrated. We're hoping that this significantly cuts down on the ESC issues going forwards.
Also, while you have the E-tube open, see this post and check the wire resistances.
If neither of those things work, then........ I don't know.
As to the "gas gauge" bars, on older software builds they were calibrated for the old C-cells, which had the ROV running at 12V. The newest build (2.5.1RC5) has a feature where you can calibrate the gas gauge for whatever type of battery you are using.