How are you judging that it is a 1024x768 image?
If it is consistent that one set of images produces a small result image, can you upload a set of such raw files to www.dropbox.com and post a public share link, here?
Because it says so in Lightoom - it prints out the dimensions as an overlay.
The original RAW CR2 images are 5,472 x 3,648. The merged HDR says 1024x768 (and it most definitely is).
Take note it only occasionally happens though, most of the time this tool it works very well. If any Adobe developer is looking it seems to happen when memory is running quite low but I can't rule this one out.