Merge Dimensions don't match original file

[vrticalmedia]

Hi,

I've been using SNS for 3 years and all of a sudden the software is not merging the images correctly. For my images, the dimensions should always be 4000x3000 and they are coming out random sizes on some(3868x2272 for example). I put the same images in Photomatix and it is merging them correctly. I'm in post-production for a client right now, so a response/help would be greatly appreciated.

[vrticalmedia]

UPDATE: Unchecking "Aligning Images" under Batch Process resolved the issue.