Rest assured, this rounding difference will not unnecessarily flag your return. In fact, the IRS absolutely allows it to make figures easier to deal with and lessen the chance for arithmetic errors, as long as all amounts are rounded consistently (which the program does for you).
Per IRS instructions: "You may round off cents to whole dollars. If you do round to whole dollars, you must round all amounts. To round off amounts to the nearest whole dollar, drop amounts under 50 cents and increase amounts from 50 to 99 cents to the next dollar. For example, $1.39 becomes $1 and $2.50 becomes $3. If you have to add two or more amounts to figure the amount to enter on a line, include cents when adding and only round off the total."
In Forms mode, I tested whether an override was possible on Form 8949 to include cents in the total. Unfortunately, the program will default back to a whole dollar to be transferred to the Schedule D, so you will not be successful in attempting to manually change the amounts. But again, this rounding will not cause any undue problems for the IRS, in and of itself.
