I do have a suggestion, but first my advice would be to take a look at the amount of the discrepancy and see if it is making any difference on your "bottom line" - meaning your actual tax due. So, if it is increasing your taxable income or decreasing your taxable income (as I am reading this to be the case) enough to actually put you into a different tax bracket (higher or lower) than you should be if this rounding issue were not present, then you will want to manually adjust the amounts so that you are not experiencing this rounding issue. There are other "tricks" to this so-called trade that you could also try - tricks to the system in order to calculate your taxable income so that it is not affecting your tax bracket - but those are merely tricks and not advisable.
Having said all of that, it is highly unlikely that the difference due to rounding is affecting your actual tax bracket and thus tax refund or tax due amount. If it is, it cannot be by all that much as TurboTax can only handle up to 500 imported transactions and if at the very worst all 500 transactions were rounding up or down all in the same direction, $500 barely - and I mean barely - has an effect on your bottom line due to the actual calculation of coming to the effective tax rate. I know this is not a "perfect" solution, but until brokerage firms and tax preparation software companies fall in line with using the same type of software, this will continue to be an ongoing issue (unfortunately).
