I'm shooting triplets for HDR with my X-E1 then processing both singles and batch in Photomatix. I noticed some results didn't seem consistent although the results are good. I found out if you use the export tool (plug-in) within Lightroom to process an HDR file the RAF will be processed by LR then run through Photomatix. If you open Photomatix and and pick "load bracketed photos" then drag or select the photos to go into this box, the RAF will be processed by dcdraw (open source) and then run through Photomatix. I did a few comparison tests and using the same Photomatix preset, the results were indeed different. Both looked good but had different curves even after going through same preset. I'll post a blog entry and reference it here once I understand more about this. There are probably members here than can enlighten me more.
Last point for now; it appears that you can't batch process with Photomatix and use the LR export function. If true, then batch will always be using dcdraw. I'm currently awaiting a response from Photomatix to be sure this is true. In any case, both processing yields good results; I slightly prefer dcdraw result after limited testing. (Iridient Developer raw processor is built on dcdraw.)
If this is also part of your workflow and have more to add please share.