You cannot save JPEGs as 16 bit in any application. JPEGs are 8 bits per channel. When you open an image from Bridge in ACR and you click on the hyperlink and set up your image export parameters, you may choose 16 bit. However, if you click on the "Save" button in the bottom left corner of the ACR window and choose JPEG and save, you will generate an 8 bit JPEG. CHeck it yourself - open any one of those JPEGs in Photoshop and I can guarantee you it will be 8 bit. Now, if you want 16 bit per channel files, save the ACR'ed RAW files as TIFF 16 bit. Now you can take those 16 bit TIFFs into Photomatix and do your thing.
Now the $64,000 question is: According to your workflow description above, you use Bridge to convert RAWs to 16 bit TIFFs, combine those TIFFs into an HDR dataset within Photomatix, do no tonemapping in Photomatix but save the HDR dataset in Photomatix. THen you take that HDR dataset and open in PHotoshop to tonemap it (i.e., convert from 32 bit down to 8 bit, using Local Adaptation). Sooooo, that begs the question: why use Photomatix at all?
You can simply select the exposure sequence of RAW files in Bridge and choose (in Bridge):
Tools > Photoshop > Merge to HDR
which will merge the RAWs into an HDR dataset within Photoshop. The result will be a 32 bit document in Photoshop ready to be manipulated or simply tonemapped via changing its mode from 32 to 16 or 8 bits per channel. I would advise you to save the 32 bit file before converting to a lower bit depth, in case you want to tonemap a different way in subsequent processing, without having to combine the RAWs and merge them repeatedly. Photoshop also does automatic image alignment during the merge process.
No muss, no fuss, no Photomatix necessary. That's some He-Man, Castle Grayskull power right there.