This is how I understand it although I am not an expert. All funds removed from a traditional IRA are taxable as ordinary income. As far as I know, if you convert traditional IRA to ROTH there is not a tax on this conversion to ROTH when it is big. Later, when you do withdraw from ROTH, even if is years from now, there is no tax because you paid tax when you contributed to ROTH.
What you may be encountering is a new rule - If your total income exceeds 250,000.00, due to a larger than usual (do not know what constitutes usual) withdrawal from trad IRA for conversion to Roth, there is an additional tax on the IRA withdrawal amount that causes your income to exceed 250,000.00. It is reported on line 23 of form 1040. I believe it is approximately 3.2% of IRA withdrawal causing you to exceed 250,000.00. This is not a tax on Roth contributions - my understanding is it is part of having wealthier people pay more tax.
Don't know if this fits your case, but it may explain what is going on.
