I suspect that you've entered both a $43,000 60-day rollover and a $43,000 CRD repayment (indicating that you put a total of $86,000 back into the IRA). Click Tax Tools -> Tools -> View Tax Summary -> Preview my 1040 and see if you see a ROLLOVER indication on line 4b indicating that you reported a regular $43,000 rollover. Try deleting and reentering the Form 1099-R.
If the $43,000 was put back by the regular 60-day rollover deadline and would not result in a violation of the one-rollover-per-12-months limitation, you would probably be better off reporting that $43,000 as a regular rollover instead of as a CRD repayment. That would permit you 3 years to repay the full $100,000 CRD later instead of being able to repay only another $57,000 later.
