I love latex printers but this is their biggest weakness....They use heat to cure the ink which is very sensitive to environmental changes, temperature, moisture, print speed, and so on. And because the printer runs over a period of time the latent heat at the beginning of a run is cooler than after is has been printing for awhile. I used to use an HP L28500 and it was way worse then the latest series of HP latex printers. My old one didn't use optimizer or have an on board profiling system, HP added those features to alleviate the issues you are having. So the solution sounds complicated but in practice it's very easy.
1. Print your panels in installation order...i.e. print panel 1, then panel 2, then panel 3, and so on. This minimizes the color shift as the printer heats/cools throughout the run. Any color variation is hidden because the panels that need to match were printed next to each other.
2. Rotate every other panel by 180 degrees. That way the left side of say Panel 1 prints on the same side of the printer as the right side of Panel 2. This helps minimize color shifts because as the printer begins each pass either left or right it takes a split second to be jetting the inks properly...so the left/right edges might have a color shift before the jets are firing properly. Also in a latex sometimes the heating elements are a little hotter/cooler on the left/right of the machine, this is more common the older the heating element gets and wears out. But rotating every other panel allows the right side of one panel to be on the same side of the printer as the left side of the next panel...reducing any color shift.
3. Lastly add a small printing gutter to each side of the prints. It's an option in your RIP software. This prints pure inks (CMYKLcLm or whatever your inkset is) in small strips along the edges of the roll. Again because the latex gets so hot and is so sensitive to environmental conditions that if you are running a print that is using heavy amounts of say Cyan but not much Magenta, then over the course of the print run the Magenta head is exposed to a lot of heat while not firing a lot of ink. Then when it comes to a point in the print job where it needs to fire the Magenta the heads take a bit to recover and fire the jets fully. But if you have the printing gutters then the heads a kept "fresh" and constantly supplied with ink and not drying up with the heat.
It sounds tricky but it's simply a matter of printing in order, rotating every other print 180 degrees, and clicking a check box in the RIP for the gutters. This will minimize any color shifts, and honestly I do these on all of my paneled print jobs regardless of the printer technology it's just a good practice and yields the best results reliably.