I have rotated all of my images (3300+, actually ~9999 these were converted to HDR) in LightRoom 5 before i exported them to Photomatix for hdr processing. After the hdr processing all the images are still in their correct perspective (not upside down). When I initialize them in LRtimelapse they are upside down again. Why is this? I am going to assume that LRT cannot read the metadata for the rotation. Will they be correct when i reload them in LR5?
By the way these are jpg; 9999 raw images would be insane to work with.

Thanks

The rotation flag will be supported in the next version, but anyway you are not going to see the rotation in LRTimelapse.
Tip:just rotate the images to the right orientation in Lightroom before exporting the video.

They are already rotated from lightroom. It is just when I installed them in LRT that they went back to their original perspective (upside down). And even when I look at the images in the folder they are correct. It is just while they are being viewed in LRT that they are upside down but you said that LRT does not read the rotation flag yet. I will check them before exporting to a video, as you have said.

Thanks