I struggled with this for hours - if you're having this problem allow me to enlighten you.
1) Set your Behringer to 44.1k clock, not 48 - The whole setup does not play nicely with 48khz!
2) Set your Saffire Pro to the same in Saffire MixControl
3) In Cubase Audio Device setup ensure your Clock Source is set to ADAT
4) On your virus in CONFIG ensure that Audio clock source is set to AUTO - if you see the option to select 44.1K or 48K - obviosuly set it to 44.1k
Thats it...
I set my clock to 48k on the Behringer and the Saffire pro - it all went out of sync no matter what I did.
When I tried setting everything to 44.1K it syncs up nicely again.
Cheers.
Rob.