It turns out that if you are self-employed and contribute to Traditional IRA and then you make a contribution to a Traditional SEP and file married-filing-jointly and the joint income is over $143k, TT will not deduct your Traditional IRA contribution anymore, so that is why you see an increase in the amount of taxes you owe (or a decrease, if the sum is green). You need to dig through the forms in TT to see this. Based on some research online, this seems to be correct: you can't contribute to both Traditional SEP and IRA if the joint income is over $143k. So, pick one, or contribute in Roth.
