I am using LR3.6 on Win7 64bit. I have found a bug in the Print module. The template browser does not save the selected printer profile when creating a User Template. I am using an Epson R3000 printer with driver version 6.71.
So after your post, I selected a template that saves the print job to a file (instead of printing) and found that the printer profile came up. Then I recalled a template that prints directly to the printer & the profile is now coming up! The profile is coming up on all my previuosly saved templates - even after re launching LR and also rebooting the computer. So the problem is solved for now; but I had been experiencing this problem for a few weeks so I know that it is real.
I have experienced the same problem (Template browser does not save the selected printer profile when creating a User Template) using the LR4 Beta on my laptop running Win 7 64bit. This time the solution was to update the template to save to a file and then reupdate it to print directly to the printer.