YNAB tech support people are excellent. I'd suggest you email them about your multiple bank accounts. It could be something the import system is doing weird, and they might know of a work around.
I don't pay much attention to cleared/uncleared balances. For your transfers, it's important to make sure each transaction only shows up once in each account, an Inflow in one and an Outflow in the other. Delete any duplicates.
You may find that with YNAB you don't need to use bank accounts as envelopes. If you spend from your budget (making sure you have enough in your working cash account to cover everything) the budget will serve as your envelopes. It may take a few months to transition over, and transitions are always messy. Stick with it, as YNAB is an excellent system.