Multiple Superannuation Funds

Hello,

We have an employee who has multiple superannuation funds, one that his superannuation guarantee is paid to and the other which they salary sacrifice a small amount too.

As MYOB does not support multiple funds the workaround until now has been to have a primary card and a secondary card, with a salary sacrifice-split set up under deductions on the primary which flows to the secondary. Unfortunately, commencing this financial year it is resulting in an STP issue ATO error code: CMN.ATO.PAYEVNTEMP.000389. The derived aggregated gross YTD amount must not be a negative amount. The secondary card does not have a wage as it is purely as a workaround for the payment to the second fund. 

I have spent hours on hold with MYOB support, and they have informed me to contact the ATO. The ATO tell me it is an MYOB issue. 

Has anyone else in the community had this issue and found a suitable solution? Thank you