sounds like they did a bit more than just a trans service and fuel system service? because you then state :rear main & trans cooler? this means the transmission was removed and re-installed
at any rate depending on the condition of the transmission and previous transmission services doing a flush can dislodge material that then gets into places it wasn't before and then you have a problem, bottom line transmission flushes being done at high mileage and not on a regular basis can in some cases be risky I would speculate if you are under 80k then you might be ok. yes the owners manual says up to 100k intervals but that all depends on how it was driven and how long it has been. I always recommend a annual flush even if you only drove down the street and back.
if the noise is indeed coming from the transmission then you will need to have it pulled out and inspected (at the very least) and most likely rebuilt in some fashion depends on how much damage there is inside. guessing and asking online what do you think it is? well it's the transmission sir.
Transmissions have a lot of parts inside, high fluid pressure and very tight tolerances even a small spec of metal can cause problems.
report the problem to the dealer that serviced it and see what they find.
having the transmission pulled out and inspected typically runs about $500 but most places will apply that cost towards a rebuild.
good luck.