I noticed that too. It happens because in the GUI the initial page orientation is determined by the thumbnail image w/h ratio, and here the thumbnail already has the 90 degrees applied. The code that generates the PDF, if the page orientation has not been determined yet, calculates that orientation inspecting the PDF page media box itself, and that way it works. But this second method can't be used if the GUI already provides an orientation, because user may have changed it.
But all this is, thanks to your report and sample files, now fixed, so in the next release it will be a non-issue. Meanwhile you just need to manually assign the portrait orientation to all these PDF internally rotated pages.
