Patrick,
My users also report issues with pdf caching. It only happens intermittently for me. I asked about it at the Flex Viewer island last week at the ESRI UC and the response was, to paraphrase, "sounds like it is holding it in cache" (duh!) but no solution was offered or even brainstormed. It was an atypical response from what I have come to expect from ESRI employees.
Unfortunately, I didn't have time to get back there in the hopes that another employee might have a better response.
I also do not have any issues updating my custom templates for the ExportWebMap gp task. I believe the help documents two different methods for creating and storing the templates. The method I used was to create a folder on my network to store the mxd map layout templates. This folder is not on my map server but in a folder that is registered with the map server. I have updated my layouts various times and once saved they are immediately used by the next print request.
BTW, I am still on the 3.0 version, working on getting the 3.3 (well, now 3.4...) version rolled up. The pdf caching issue has apparently existed since the gp service was first added to the API.
I would love a solution, as I am getting "beat up" by a few users who extensively use the viewer in their workflow.
Brian