When you say the fan was running - do you mean the interior fan or the FBH fan? (sounds like a jet turbine when it gets going?)
If it was definately the FBH fan then in theory the FBH itself must have been firing because the flame detector would stop the fan from running after a few seconds.
The FBH has its own pump which runs at the same time as the Aux pump (if the aux pump fails the FBH wont overheat etc) and as you say, I replaced the Aux pump last year (with a genuine jobby)
Did you let it run for the full time? I believe (but am not 100% sure) that the FBH heats the engine first, then when it reaches a certain temperature, a valve opens to allow the interior to be heated. Maybe the engine wasnt up to threshold temp?
You can check the aux pump by turning the engine off when it's fully up to temp, take the key out the ign and press Max AC - this runs the Aux pump and the blower fans to keep the interior warm (not using the FBH though) I found the air from the vents was cold after a minute or two where as it should be nice and hot.
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