I think you have slightly misdiagnosed the problem. /etc/rcS.d/* are run in all runlevels, not just single user mode. (Single user mode runs /etc/rcS.d/* and /etc/rc1.d/*; multiuser mode runs /etc/rcS.d/* and /etc/rc2.d/*.)
However, you seem to have the same symptoms as bug 448095, which is caused because resolvconf starts after ifupdown. I will mark this as a duplicate for now.
I think you have slightly misdiagnosed the problem. /etc/rcS.d/* are run in all runlevels, not just single user mode. (Single user mode runs /etc/rcS.d/* and /etc/rc1.d/*; multiuser mode runs /etc/rcS.d/* and /etc/rc2.d/*.)
However, you seem to have the same symptoms as bug 448095, which is caused because resolvconf starts after ifupdown. I will mark this as a duplicate for now.