The 1099-r causes my refund amount to significantly decrease. I removed the Federal Income Tax Withheld to see what it would do and the refund goes up. Any idea why?

if your marginal tax bracket is higher than what was withheld when you took the taxable distribution,  you owe more now.   

let's say, upon distribution, the administrator withheld 10% of the money for federal tax.  But you find yourself in the 22% tax bracket.   that would mean you owe more tax than was withheld. 

Or..maybe you are mis-reading the "Refund" monitor

...and it's really a "Balance Due"...and the Balance Due amount increased.