Effect of IRA EOY balances on RMD and Social Security taxable amounts; incongruities!

Over 30 years using TT (Parsons before it was that) and I cannot figure out what is going on. Initial return showed full refund of all WH, until I entered EOY Balances on 8606 for T-IRAs. Have $52K in SS earnings; $58.8 in RMD distributions; total $138.8K.

Scenarios:

1) w no balances entered, shows $1642 SS taxable.

2) w balance of 1.1 MIL (T) and ZERO (S), shows SS taxable 12.7K and RMD taxable 16.5K (21% of total income).

3) If I change to "actual" balances of 380K (T) and 725K (S) -- which is still 1.1 MIL -- the SS taxable is 42.5K and RMD taxable is 51.6K (68% of total income)!!  

So what is going on??  The amount of income doesn't change, the TOTAL balances are the same; why does the taxable percentage jump from 21% to 68% with no other changes???  Anybody got a clue? I'd like to fix this as my refund of almost 6K completely disappears in Scenario 3. (and we could use it!)  HELP PLEASE!  BobW75087