Addendum: I was contacted by a photographer last Friday who is using Lightroom 3.6 to Batch Process his Bracketed images for Tone Mapping in Photomatix software. His problem is that the Frames just don't line up. Lightroom 3.6 belongs to my Daughter and is on her Laptop. Had a look at the problem yesterday as she is at home for Xmas. The issue seems to be that he was not actually correctly executing the Batch Process technique. I had to jog my mind but this is how I would do it (there are probably other ways that may be better/easier, but this works):
(1) Identify the 0 EV frame from the Thumbnails displayed at the bottom of the screen
(2) Single Left Click on the Frame and then go to Develop
(3) Fully process this 0 EV Frame, then go to Settings in the top Tool Bar and Copy Settings
(4) From Photo in the top Tool Bar, click on Add to Quick Collection +
(5) Return to the Thumbnnails at the bottom of the screen and in sequence, highlight each Frame to be Batch Processed and use the sequence Photo, Add to Quick Collection + to assemble the required Frames to be Batch Processed
(6) Quick Collection+ can be easily located in the Library tab under Catalog
(7) Open the Quick Collection + file and highlight all the Frames to be Batch Processed (Hold down the Shift key + Right Arrow)
(8) Open the Develop tab on the top right of the screen, go to Settings, Paste Settings, tick all the relevant boxes and click on OK
(9) Return to Settings and repeat the exercise for Synchronize Settings
(10) Batch process the images by going to File and then Export. All the images will now be found in a Folder labelled LR and will be ready to be input to Photomatix

My colleague was probably not using the Synchronise Settings instruction. I actually do not use LR3 myself, so I am not nearly as proficient as others who use this software day in and day out.