A couple of quick comments (that might not be relevant, because I don't know much about the Windows world these days):

(1) The old Tom Christiansen pod processing code is known to have some problems, but it's taking a *really* long time for a replacement to become accepted. I suggest taking a look at Pod::Simple::HtmlBatch. I posted a review here a while back: Pod::Simple::HtmlBatch.

(2) A gotcha that took me an embarassingly long time to figure out: Don't indent a list of L<> links. Indentation means "code block" in pod-land. (But it doesn't sound like this is your problem).