I have never tried doing what you are soing so I am just thinking aloud. I think that using datamerge for this is going to assign the same ID to the fields, which is why the checkboxes are filling when selecting one of them. Open the PDF in Acrobat to check it though.
Another thought. Are you merging to a new document or direct to PDF? If going direct to PDF, try creating the merge document first. If that doesn't work, I think it will be the field IDs being also replicated. If so, then the only course of action would be either manually changing them in Acrobat, or an ID script and or an Acrobat script. Neither of which I have heard of. But if they do have the same IDs, then I would inquire in both the ID scripting forum and the Acrobat forum.
Good luck. Interesting use of datamerge. I hope you find a suitable answer.
Thank you Mike. I am creating a merged InDesign document first and then exporting to interactive PDF. I imagined that I could manually add the check boxes in the PDF after the fact but that seems like a lot of work in a large listing. I was hoping to avoid scripting as I am not at that level yet and I don’t even know if it is possible even if I was. I think this would be an excellent feature, to have the ability to place interactive fields, buttons and check boxes in each section of a data merge document which each function independently. Hopefully Adobe can add this useful functionality in the future.
Also thinking out loud. Can you add a glyph or some unique type to the data you want to merge (xxx for example), then to your merged InDesign file, do a Find/Change to the unique text and change it to a check box you have copied into your clipboard? (Change> Other> clipboard contents).
I'm also trying to do this. I have discovered that you can put the form elements on a Master Page and then just assign that Master Page to the Merged into ID document. From there, then you can create the interactive pdf. But it sure would be nicer if the data merge script gave the interactive pdf option right from the start!