I was about to launch your dokan market place, but seem like there are a lot of thing need to fix before that.
I'm having the same problem, whenever i enabled the shipping per product it will bring me to the error
‘shipping was not chosen' , it not accepted any other shipping class other than dokan shipping.
Problem is, when it's go to the variable product, they couldn't set shipping using the per shipping. my seller have to rely on the shipping class that i fixed. In this case, i can just desiabled the per shipping http://wedevs.com/support/topic/shipping-3/
I'm planning to launch the website by end of this month, i hope before that i can get all this fix.
Please go to WooCommerce->Settings->Shipping->Shipping options and check if you have selected and activated Dokan per product shipping. If you have already enabled and set Dokan per product shipping as your shipping method and you are still getting the error please let me know.