When I set up a simple flow model with a surface temperature "source" applied and run the simulation I can get an average heat flux for that same surface. However, when I turn around and run the same model with that new heat flux value as a "source" I don't get the original temperature value back out. I'm essentially trying to run a check on the first simulation and don't feel confident that it's correct.
Basically, I need the heat flux value because i'm going to place this single part into another more complicated assembly model that's a closed volume enclosure and ultimately want to find out what the operating temps will be. So in that model I of course won't be able to apply a surface temperature heat source, but rather need to apply a heat generation value.
Is it possible that some of your surface heat is conducting through your solids and being cooled off by a different part of the fluid? Are your temps higher or lower with the surface source than with the temperature source?
I would try using a volumetric source instead of a surface source as well, see how that affects your results.