My work flow is as follows:  Shoot in RAW (5DII). Open in PS CS6 RAW convertor.  Make whatever adjustments needed to all images simultaneously.  Save as TIFF.  Open the TIFF files in Helicon Focus and let it do it's thing.  Save output as a TIFF file.  Open this TIFF file in PS CS6 and finish any post processing, including adding all metadata.  Never had any problems following this sequence.

what exactly do you mean by dual and washed out?

- I first make the RAWs adjustments in Lightroom. I find that it is better to work on images already well exposed and contrasted, with a correct white balance, before to start the work in Helicon Focus.
It is better to not use any kind of lens correction, distortion, effect, crop and local brushes (gradients, spot removal, etc) in Lightroom, better to do only the basic RAW adjustments.

-Then I export in jpeg higher quality (no need tiff or else because the images will not be re-saved in jpeg then, so they will not lose quality, and with jpeg the job is faster in Helicon Focus when you have stacks with a lot of images)

- I import the images in Helicon Focus and chose the method (B is the one I use more, but it is not necessarily the best for all situations), then I let the software to do the job, and I save the result with a descriptive name in psd format.

- At last I open the psd file in Photoshop and do some necessary adjustments (generally I have to correct a little the levels to �pop� the image because, yes, it can appear a little dull sometimes).

- Once I am satisfied I trash RAWs and jpegs.

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Once the resulting image is imported in Lightroom I put keywords, title and description, and it is ready for the microstocks.

As pointed out by Beppe, it is better to make the adjustments first in LR, and export them as TIFF or JPG files for Helicon stack processing.