Apologies for immediately assuming that the problem was on your end, as it turns out, this is a bug introduced with the fixes posted for v2.52. I'll spare the details, but the gist of it is that an if statement was worded incorrectly, causing the dual wield sequence to lose the offhand weapon. I have corrected this in v2.53, which should now be up for download.
The other issue with turning off the barehanded attack causing both swings to look the same is also a bug on my end, and apparently has been like that since I implemented that plugin parameter. A check that checks if the wielder is dual wielding fails at a certain point during the dual wield sequence, which causes the script to continue with a second attack, but assume that the actor is only wielding one weapon, making both hits main hand swings only.
I have also corrected this issue in v2.53. As I said, the download should now be available, so feel free to verify that it is now working.