I have a pumpkin ale in the keg right now that went really well that I did in an all-grain batch. I couldn't figure out how to properly incorporate the (canned) pumpkin into the mash so I calculated my infusion temperatures without the pumpkin. Then, I added the cans to some brewing liquor in a separate pot prior to doughing in, heated it up and stirred it up until it was a consistent "soup" and I was at the sacc rest temperature. Then I started the mash as usual without the pumpkins and after I had hit my mash temps, added the pumpkin "soup" at the same temperature.
Now, with REAL baking pumpkins this is going to be a bit harder - I would suggest baking the pumpkins in the oven until they really break down to a similar consistency as the stuff in the cans and proceeding the same way.
However, the impression I'm getting here is that you put it in the boil. I've never really understood why that would be necessary - Pumpkin *does* have a flavor itself, but its actually quite vegetal for lack of a better word. However, if you want to do that, I would suggest trying to cook down the pumpkins in the oven a little longer until you can really really break down the pumpkins into a little more. I wouldn't really worry about the flavor in the primary, either. If the pumpkin was going to add a bunch of weird flavors would probably have already been imparted by boiling the pumpkin, and you said it seemed to taste good.