Ok guys,
I don't understand your problem, it works well with same settings from
DeafEyeJedi.
@DeafEyeJedi could you try to launch export from folder M20-1628.MLV and not from Previous import ?
Could you post screenshot from summary dialog?
Please, tell me how do you obtain your DNG files ?
Could you check keywords?
(if you have no Dual-ISO, plugin skip)If file isn't available, plugin skip too
Could you share 2-3 dng files from your sequence ?
or
Could you share a MLV that have problem (I think you use MLVFS)
I'm not a filmmaker, so I didn't test the plugin with it, I need to test it!
For Mac Users, could you paste me the log from Console.app (located into /Applications/Utilities, search Lightroom) and I need for the moment only line start with command. Windows users are welcome too

like this:
28.09.14 09:28:32.236 Adobe Photoshop Lightroom 5[44598]: MLDualISO DEBUG command : exec "/Users/tof/Documents/MagicLantern/LR plugin/cr2hdr.lrdevplugin/bin/cr2hdr20bit" --amaze-edge --cs2x2 --really-bad-pix --fullres --alias-map --stripe-fix --wb=graymax --same-levels "/Users/tof/Pictures/Photographies/ML Dev/Dual ISO/_MG_12826.dng" "/Users/tof/Pictures/Photographies/ML Dev/Dual ISO/_MG_12827.dng" > "/Users/tof/Pictures/Photographies/ML Dev/Dual ISO/_MG_12826-_MG_12827.TXT"