I find that the easier way to calculate savings rate with YNAB is to look at total spending for the month. That way I don't have to worry about contributions to 401k, FSA, etc.
Spending + Taxes + Savings = Gross Income (in theory).
Assuming you don't have a variable paycheck, I would expect your taxes to stay the same each paycheck (barring a change in 401k contributions, insurance, etc). Just look at a paycheck and see what your total taxes are. Then, you know all but one of the variables above. You can then plug the numbers in and get:
Savings = Gross Income - Taxes - Spending.
Savings % = (Savings/Gross Income) * 100.
So really, all you need to do is know your gross income and taxes (constant from paycheck to paycheck), and then just look at your total outflows for the month in YNAB.