Hi, those are the measurement guides you use to set how far the rail is set back from the edge.  You need to follow the calibration instructions to set the measurement guides up.  There is a slot in the router base plate that attaches to the rail which you use to set up the measurement guides.  There are plenty of video guides on youtube, and there are also some guides on the forum. 

try this


Regards
Bob

The slight difference in lengths is a non-problem since you should be calibrating the position as described above by @bobtskutter .

If this is known info already then it doesnt explain the out of square issues you are having. rod length doesnt matter as long as the scales match up.   

The OP - per own admission - did not have the rods calibrated and his scales were shifted ..

Yeah, the length of the rods not matter, what matters is their position is calibrated so the scales match. But you know that.

Could it be that they are different length so that you can tell them apart once they are calibrated?

I'm a novice wood worker.  I don't find the LR32 system easy to use, because i don't use it everyday.  Please allow me to share some of my learnings.
1) Follow Sedges guide to set up the rods, make sure the block that attaches to the guide rail IS attached to the rail and make sure the locking nut is tightened up.  The locking nut doesn't need to be "white knuckle tight" but it does need to hold the block on the rail.  Make sure the block is sitting FLAT in all directions, I've found the block doesn't always sit flat on the rail.  Make sure the block with the guide pin is pushed down flat on the workpiece and not forced into the cut out on the router base plate.  Sedge does SHOW this in the video.  The guide pin is spring loaded so if it's pushing DOWN on the bench is cause the rod to lift up.
2) When you're using the system, make sure you set the same number on both rods, e.g. 37mm on BOTH.  It's very easy to set them up incorrectly because of the black measurement scale on the moving block with the pin.  Put the rods on the guide rail as far apart as you can and make sure they sit FLAT in all directions (see point 1).  Make sure the locking nut is tight (see point 1).  Make sure the pin is touching the edge of the workpiece, try not to bang the pin against the workpiece, it can make the rod lift up.  Watch out for the pin pushing down on the bench below the workpiece.
3) CLAMP THE RAIL TO THE WORKPIECE.  This is important!!
4) I then swap the rods around to double check the alignment before I start drilling holes.
5) When you attach the router to the guide plate make sure the attachment screws are tight so the router doesn't move on the plate.

The more you use the system the better your skills become and the faster you get at setting it up.

Regards
Bob

Out of curiosity, I just went and checked mine. One is 276mm the other is 278mm

As others have said, once calibrated it shouldn't matter.