2006 Chevy 2500HD Duramax/Allison LBZ motor.

29,500 miles

About 3000 miles ago it threw a "reduced engine power" display and put it into shutdown (1000rpm total, no changes) mode.
They found a connector that was bad/chewed up by the master cylinder.
fixed

Now, in the last 50 miles it has started throwing a "change fuel filter" on the display and that would be fine except
a.  I just changed it 5500 miles ago and b.  I haven't gotten any diesel lately, nothing has changed (and I buy at the same fuel stops that's running fine in my semi's and tractors)

And yesterday it threw a "reduced engine power" while driving along.  
I drove right over to the dealer before it went dead on me.  (last time I had to load it on the semi to get it there)

Shop called and said "we see it threw the codes, but we can't recreate it"

WTF is going on here?

need some ideas to throw back for them to try.
This is my winter plow truck, it simply can't go down at 3 in the morning.

Take a fuel sample.

I had a customer with a very similar issue last year. You more than likely have a heavy load of soy oil in your fuel. Clogs up Duramaxes like you wouldn't believe. +1 to taking a fuel sample. If that's not an option, get some Iso-Heet to help keep the fats from clogging the filter while you burn this tank off.

thanks, I'll suggest that.
where would I have ended up with soy oil?

Diesel fuel can contain up to i think 11% soy oil before it's marketed as biodiesel. When I was at the dealership, we had more than one occurence of the regular diesel at the fuel station across the road being particularly heavy on soy, up to 50% once, had something to do with the tanker that brought it in having hauled a load of pure soy oil and not being cleaned before taking on fuel. I know it's a stretch, but it's happened here.

One thing about ULSD and Bio...It will clean EVERY bit of shit out of your fuel system. Every single chunk ends up in the filter. I got so sick of changing filters I was ready to burn the trucks down in the lot. It took about 6 months and then the systems went back to normal. We still are having some problems up north where a few states require Bio diesel.

As an FYI...We change all fuel filters every PM. That is 4 months or 12K. When the problem showed up we were lucky to get 2-4 weeks.

Chris