For TX Franchise Tax reports on LLC (or other corporations) we have a similar problem. One state filing per 1040 return even though there are 2 or more required state filings for single member LLCs. [ This yr Intuit also would not allow us to file the state return before filing IRS on some forms (1120s, 1065, 1040)-claiming that IRS wanted to make sure that IRS was not cut out of the filings]

Intuit does not allow me to do any past the 1st one so I do the extras directly on the State Comptroller website. Not having the carryover info from prior yr is a draw back but usual they are the easiest to file so it is not a real bad situation. And usually these qualify as "no tax due" since they are low gross proceeds entities.

Good Luck