your post asks where to input the % for the state - have you done that - if you edit the 1099-DIV then hit continue after the screen with the boxes you will be asked for uncommon situations/adjustments and there will be a question for US Gov Obligations and you can input the $ amount to exclude.
Tho if you haven't done that I would expect 100% to be included in state tax not excluded. If you're still having issues try inputting the 1099-DIV manually and see if that works and delete the old one, there have been a few threads of folks reporting issues with 1099-INT/DIV not hitting their state tax correctly for either munis or US Govs, usually due to some import issue.
Not sure what rule Bill is referring to that over half of a fund in US Govs means all of it is exempt. There are rules in CA, CT and NY that at least 50% of it must be in US Govs to qualify for any exemption.
