IRA RMD Incorrect Penalty?

To make the numbers easy, let's say I have two IRAs with equal amounts and I have a total RMD this year of $1,000.  I decide, as it is my right, to take $100 from account #1 and $900 from account #2 to satisfy my RMD.

 

For account #1, I enter $100 from my 1099R and TT asks what my RMD is for that account.  Well, theoretically, it is $500, so I enter $500.  For account #2, I enter $900 from my 1099R and also fill in $500 for account #2's RMD.

 

TT will then assess me a penalty (25%) on the $400 that I am under-RMD-ed on account #1.

 

This is incorrect.  TT should be asking me what my total RMD is AFTER I enter in the 1099R information from all my 1099Rs.  Had TT done that, I would have entered $1,000 for the total RMD and that would have matched the sum of the $100 and $900 1099R distribution amounts.

 

The way TT phrases the questions is somewhat misleading.  The workaround appears to be that I simply "lie" and enter $100 as the RMD for the account that I took $100 out of and $900 as the RMD for the account I took $900 out of.

 

Explanation???