It seems some bacteria also give black center growth on Salmonella-shigella agar. My samples where positive for salmonella based on culture confirmed and biochemical test however, I couldn't amplify aroC gene and fliC genes(S. typhi) in my samples.
Proteus spp. may also appear with black centers on SS and XLD agars and give similar to Salmonella reactions to some tests during biochemical confirmation (e.g. on TSI agar for utilization of lactose, sucrose and glucose).
That's why serological confirmation and more biochemical testing is needed. Furthermore, molecular identification and confirmation of Salmonella should be more reliable than any other biochemical test used, so if you don't get PCR products then probably you should consider not having Salmonella either isolated or in your samples.