I realize most do not use codes, but knowing they are there can be helpful. You need to be sure that the SDI for job 1 is entered as SDI and the VPDI for job 2 is entered as VPDI. See the image for the two entry points.

This will create the overpayment of SDI credit on the 540. It will add the SDI to State Tax Paid on Schedule A, but not add it for VPDI. Putting both as SDI will likely elicit a letter from FTB about an error on the return, since as previous pointed out these are definitely two different flavors of the same thing.

You should not be hunting for a fix. IT AIN'T BROKEN..