My guess is that there is some issue with the advertisements in the old issues that require their removal. This was a problem that TSR had when they released the old Dragon magazines on CD ROM back in the day. I even went so far as to compare the issue I just purchased, Dungeon 139, to a scanned version on Archive.org. Sure enough, several advertisements had been removed from the version that I just downloaded. I hope if this is the case that Paizo has a plan to update these old issues and make them available for PDF purchase again. I know that's a lot of effort on their part but there is some really excellent content in those old issues.
