Sometimes the Refund Meter is not actually a very accurate indicator! It can jump up/down because you made entries in a previous section and then moved to another section (especially if you move around in the program).
If you're using TurboTax Desktop and just updated, deleting the imported 1099-R entry was a good move. Have you tried deleting it and re-entering it manually?
Be sure to enter Federal Tax and Code in Box 7, and pay attention to the follow-up questions after entering 1099-R fields.
Go to Forms and look at the 1099-R Worksheet and Form 1040; the numbers may be accurate there (not like the Refund Meter).
Click here for more info on How the Refund Meter Works.
Here's more info on How to Enter 1099-R.
Remember, you can click on Online at the top, and 'Check for Updates' anytime. Never a bad idea to clear Cache and Cookies either.
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