First I am not trying to defend Pella's actions, I am just throwing out some ideas to maybe explain their actions.
I used to install Pella windows and do remodeling work. I was always amazed with Pella's windows. Window rot and failure isn't always due to the window itself. Which may be why Pella is being a stick in the mud. If the siding or water barrier between the plywood and the siding is installed incorrectly than water can get into places it shouldn't, especially if the window is on the side of the house that gets all the rain and wind. Wind can drive water into funny places as well. Also if the window was install improperly it will leak. And in my experience there are a lot of bogus window installers out there, although Pella installers have to be certified so that may not be the case for you.
You may have also gotten a bad window. How many thousands of windows do they install every year. Probablity says a few are bound to be bad. Something else, if you have done anything to the window to fix it, Pella may legally be able to deny the warrenty. The photos in the link above look like he put spray foam on the window to seal them up again.
Sorry to hear about your experience with Pella, but I don't blame you for switching brands.

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