Im not a hardcore video editor, I just know very simple things, and sometimes not even that.
I use Sony Vegas Pro 13.0 and this is whats happening.

I have some videos I want to render separately, they were shot with cellphone camera and so they are portrait, not landscape. Media Player Classic for instance shows it correctly, although file information says width is 1920 and height is 1080 (Im guessing the cellphone rotation thing comes into play and the video player reads some metadata and plays the file in portrait, thats why it seems right).

Well, when I add them all in one track to Vegas, they start in landscape so I change the source for all the files (properties / Media tab/ rotation / 90 clockwise). I also go to project properties and change width to 1080 and height to 1920 (I invert them). Now everything looks right. All videos are in portrait and they play correctly without black strips on sides. To render, I customized a template which basically inverted the height and width of the Internet HD 1080p template. Now comes the catch.

If I render them by going to File, Render as... I select my template and render, all the videos are rendered as one file and the frame size is correct (I can also render the loop region only, ok). But as I have many videos, I created regions, so I can render them in separate files, but all at once. I go to Tools / Scripting / Batch render and select the same template, but now, when I render, the files have frame size 1440x1424 and those black strips on the sides. Can anyone let me know whats going on?