Aqua-Hot in Cold Weather - Issues with Performance?

Thanks for all of the replies.

I'll try an answer all of the questions I received. Unfortunately, I am more familiar with this unit than I care to be.

1.) Fuel nozzle and filter are replaced at least every 12 months with genuine parts
2.) Fuel lines are new, and rated for use with diesel. No kinks were present at that time.
3.) Electrode gaps is checked and set every time the burner assembly is out
4.) The wiring was not replaced, no issues with that (remember, it was a dry fire that ruined the old chamber and tank)
5.) Voltage was near 13 VDC - can't remember exactly as it was close to a year ago when this happened
6.) The computer is the new black one. I still have the old silver one and the new, toasted black one too. If anyone repairs the latter, I'd like to know who.
7.) This issue occurred at roughly 800 ft. above sea level. Normal range of operation for my travels.
8.) I am not sure what is meant about properly set combustion. There is no real way to check that without sending the unit off to Webasto. Other than it being a defective unit (lets hope not for the $3,500 it costs) the physics are fairly basic. Fuel pressure and flow rate, nozzle geometry, combustion chamber geometry, ability for intake air to reach the chamber in sufficient quantities over a period of time.
9.) It has only ever happened this once (this intermittent issue). If memory serves me right, I believe it ran in similar temperatures the year before without issue.
10.) Exhaust was normally clean - except when the issue began then a mix of grey and black as you would expect.

Once I got home and back into the garage with it, I dove into the manual troubleshooting flow chart and got to work. Sure enough, it was the controller. Trust me, I triple checked everything because the last thing I wanted to do was plug in the other controller I had and instantly wipe it out. Once I was confident enough, out went the defective controller (black one) and in went the new black controller and it was up and running - perfectly. Note I did replace the filter and the nozzle at this time too. Obviously, I was suspect of the filter due to icing, and the nozzle was nasty from the intermittent and partial combustion. It operated for the rest of the winter just fine, and has through this spring, summer and now the fall. And it better continue this way for a long time. :)

The two variables were, when compared to everything else over the last two years since it was rebuilt, fuel and temperature. I would not be surprised if certain portions of the controller are not 100% duty cycle rated. I think once it snapped to 0 to -10 for 24 hours or so, the fuel iced over, the unit could not supply consistent fuel to the nozzle and intermittent combustion began. The control logic attempted restart after restart, and this eventually deteriorated the circuitry to the point it would not operate. Just my educated guess.

Two lessons learned:
1.) Even though you've purchased winter blend diesel, don't expect it to function to these lower temps. Add a treatment just to be safe. Will it shorten the life of your filters? Sure - but most of us never use the filter capacity anyway before the annual maintenance. If this is a real area of concern for you - purchase a filter unit from DAVCO and you will know exactly when to change your filter.
2.) Save your fuel receipts. I probably should've have considered a claim for this damage as a result of bad fuel. It may have been a long-shot but I had an entire injection system replaced on a Ram ~10 years ago when it was toasted by bad fuel. The fuel supplier stepped up to the plate and paid the repair bill. It was significantly higher than this issue.

It could be as simple as improperly set combustion, when everything was changed was the burner combustion checked? Is it only in the cold when it fails and what altitude were you at?

Which controller do you have? Silver one? or the newer one from Aquahot?
There was a black controller (I think made by Spheros?) that was problematic. The newest one from Aquahot should be better but expensive at ~ $1000
There is a guy who rebuilds the silver boxes, can't remember his name but he is on ebay.

Have you replaced the nozzle and fuel filter? Check for kinked fuel line? Did you use diesel rated fuel line? What is the voltage at the unit when running? Did you replace all of the wiring? Is the exhaust clear? Any errors?

Replace the fuel line with good quaity diesel rated. Run the filter input and return line to a can of fresh clean diesel and if you still have the problem then it's not the fuel. Get input from a good AH person like Roger Burke. It's certainly possibe that you controller has gone south.