Two 45 Watt panels. OK, let's rashly assume they are working perfectly and really putting out 45 Watts each. And, that you've got them wired up with clean solid cables that aren't cutting out any of that power, so the MPPT controller is getting 90W. It's a PWM controller and I checked the connections and they are clean and tight.
In bright sunlight, maybe that's 90W at 17VDC, but the MPPT should be able to make that into 13-ish volts which would be 6.9A, if there were no losses, at 13 volts. So let's say, maybe 6A with losses and voltage differences? OK. I was being even more conservative and saying 5a.
And yes, solar panels should be able, over the course of a full summer day (12 hours long) to provide the equivalent of 5 hours at full rated power. So your panels and MPPT controller should be able to feed 30Ah into the batteries in a perfect day. An MPPT controller will have a 2-4% power loss for internal functions, and the batteries themselves will require 10-15% more power IN to replace whatever power was taken OUT. So, let's be pessimists and say you'll only get 80% of those 30 Ah, that's still a solid 24Ah that your system should be able to replace in one day. OK. I'm happy with 24a/hr per day.
And you've got a 210Ah bank, so you can put roughly 10% of the capacity (11.4 but who's counting) back in a given day of full sunlight. At that rate...I could see it taking a full week for you to recover from a weekend, but surely by then, the controller should recognize the batteries as being charged?! Yes, but that damn light is still blinking ....
Maybe there's something being missed from the picture. Some bit of equipment that's placing a load on the batteries, fooling the MPPT into thinking they aren't charged, or more easily, something is eating power? I turn everything off at the breaker panel. There is a bilge pump that may turn on for a few seconds once a week. I have a muffin fan running 24/7 in the composting toilet (milliamps of power). I haven't checked for stray leaks in about a year, but last time there was no loss of power.
It might almost pay to hook up two voltmeters, one at the panels, the other at the batteries, and note the voltage every 1/2 hour all day long, to see what the system is actually doing. And then, since sailing is the only priority in life (G) to come back on successive days and again, track what happens over several days, trying to pin down exactly what is going wrong, at what point in time. This would be a great way to see what's going on, but I can't do it now. We just had a baby 2 weeks ago and buggering about on the boat is out of the question for a month or more!
The charging may not be optimal, but it sounds like something is missing from this picture. Yes, I agree. I've replaced the batteriesd and controller and tested the panels. Te only thing I haven't done is replace the wiring.
Unless I missed it, you still haven't said how far you're cycling them, and if you're sure nothing is drawing power wile you are away. That's important. I never go below 12.4v and rarely below 12.5v.
On the flooded/vs/VRLA voltage settings? You need the specs for your exact battery, from the maker. Sometimes you just can't get the right numbers from some equipment, sometimes you need to set the switches "wrong" to come closest. And then there's temperature compensation. You're doing all the charging at 20C, right? Or oyu have a battery temperature sensor hooked up to compensate for that?