Lacerte MFJ / MFS function was messed up. 

During the tax season I alerted them.  One way it messed up was that MFJ showed federal tax lower than MFS, but the MFJ/MFS worksheet showed a tax saving for MFS.  No idea if that was fixed.

You're in california.  The program default under User Option is set to Y for "Community property state?"  

Lacerte's computation under "Community property state rules"  generally splits Wages, Sch C and Sch E income 50/50.  Other items (interest etc) are carried to the respective spouse's MFS column/file.

You can override the "Community Property State Rules" on a return-by-return basis in Screen 3 Misc.  (As a matter of practice, I always follow the "Community Property rules" and skip the allocation of tax amounts on Form 8958 on MFS returns ONLY IF  I have a duly executed Separation of Property Agreement on file.  It could get ugly if they file for a divorce and take opposition positions on property settlement.)  Once you enter 1, all items would flow to the respective spouse's MFS column (and thus MFS files once you execute the split.)  

Use this input field to override the User Option default for community property state allocation, on a return-by-return basis.

Select “1=no” to allocate all items according to the "taxpayer" and "spouse" designators. An entry of “1” will also suppress the Form 8958 for MFS filers with a filing address located in a community property state.

Select “2=yes” to net all wages and business income or loss and allocate 50% to each spouse on the MFJ/MFS worksheet. The program allocates all other income and deductions according to the "taxpayer" and "spouse" designators.