An amount from one of my Form 1099DIV is not flowing from my Federal return to my Colorado State return on Line 3. What should I do?

You need to edit that particular 1099-DIV form, and on one of the pages after the main 1099-DIV form, the software asks what states issued the tax-exempt dividends in box 11. 

You may have accidentally indicated it was all from Colorado bonds, in which case, none of box 11 would transfer to line 3 on  the main CO tax form.

Unless you held a CO-Specific bond fund, it is likely that most of the dividends came from non-CO bonds, and you should have indicate they were from "Multiple States" at the top of the page (Desktop software uses the term "More than one state" ), or checked the box to breakout the CO-only dividends.   (an example of a break-out is shown below for an NC resident)

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