First, I would call the ProSeries helpline to see if they have a work around.  Second, you might need to consider paper filing so that you can file jointly if the software is incapable of allowing a second single member LLC for CA.  If I was paper filing this return, I would choose whichever LLC was simpler to prepare on paper and let the other one roll forward in the software each year.  It would be a pain, but MFJ is often better than MFS so it would probably be worth it.  Good luck.