For example, the original (camera raw) files are 4368 x 2912. When I merge to HDR, the result is 4366 x 2910, or sometimes 4364 x 2911. It varies, depending on the three images being merged. This causes a problem with programs that depend on consistent, exact image sizes (...like panorama stitching programs).
My guess is that happens when one has Attempt to Automatically Align Source Images checked at the bottom of the Merge to HDR Pro dialog
Excellent guess! I just confirmed - that is indeed the solution. When I unchecked the alignment option, I get consistent pixel dimensions in the final images.