Deflickering tonemapped images is not that easy due to the way Photomatix (e.g. tone mapping in general) works.
If you're using the Details Enhancer you're using a local tone mapping operator (TMO) - this means you will not only have to deal with overall changes in luminosity, but also with local changes in luminosity too - eliminating these is almost impossible especially not with LRTimelapse alone (which can only correct global luminosity changes).
If you want to use tone mapped images for your time lapse, you should stick with global TMOs, read up on wikipedia to understand what the difference between them is. I am not sure, but the "Tone Compressor" in Photomatix seems to be one of those.

Best Regards
David