Make a new file

Open a register for the income Income.
Expand the blank transaction.
Tab to account field, type 'A', 
tab to select assets:current assets:checking account
enter '1', tab, tab (to next split)
tab, tab, 'E' tab to select 'Income', tab, enter '2', tab (to next split).

Observed: Checking Account split is changed to Income.  So now both splits are for 'Income'.

I guess the register is saying "Hey, the first split in the transaction isn't the in the register account.  Lemme fix that for you."  *smack*

This also happens whether the second split is for the register account or not.

This change is happening *before* the transaction is committed.

If you put the first split back to the desired account, you can move around inside the transaction without a problem, until you change the amount of the second split.  Then, upon leaving the second split, the first split will change back to the register account.

This is in r13646.