As was mentioned, if your first runnings are low, your conversion could be bad, or you have dough balls, or pockets in the mash/grist that never get exposed to the wort. If your first runnings are OK, but you require highly increased sparging to get the total amount of sugars out of the mash, you may have mild channeling issues. If you first runnings are OK, but no amount of sparging gets the total amount of sugars out, you may have severe channeling.
You say you are using a HERMS (that is what you have, not a RIMS), but don't have any probes on the in/out. Those are very helpful, and would be a worthwhile addition. You also say you are using thermos mounted in the pots. I know they say Blichmann and all, but those bi-metal thermos really shouldn't be used for precise measurements in your mash. (Waits for the impending wrath from the cult of Blichmann.) Used just as a sanity check, they are great.
Calibrating your thermos is a good idea. Pegging it to boiling water is a good calibration method for the hot side if you don't have any other reference.
What temp are you using for the HERMS/HEX bath? As long as your 'HEX out' temp is within 1-2 degrees of the mash temp, it isn't a huge issue, but I try to keep the bath within 7F or so of the mash temps during steady state. Higher than that and I worry, possibly falsely, that I am cooking enzymes in the HEX. If you are having to go higher than those temps diffs for either the HEX bath or HEX out, increasing flow or HEX size, or insulating the tun, can help. Agitating the bath also helps, for which there are many solutions.
FYI: Longer or more vigorous boils to increase boil off to concentrate the wort to get back to the desired final volume/SG is not a good way to tune or repeat a recipe. One way to compensate for a unplanned reduction in efficiency without increasing boil time or rate would be to adjust your final volume on the fly. It would require having some calcs/formulas ready, but if you notice your first runnings are not up to snuff, it wouldn't be too hard to run some new numbers for pre-boil volume and SG, possibly more than once. I started down this path when I was having large fluctuations, but that stopped after some process and equipment improvements.
Check those thermos for cal. If your issue was your wort (and beer) looking like dirty starchy pasta water, I would say your thermos had you mashing 15F low. Take a wild guess how I know.