Note that the final versions of both the console-common and console-tools packages include checks for console-setup, and if present their init scripts are supposed to be no-ops. So if disabling the rcS symlinks for these fixes the problem for you, it's possible that you had removed these packages by hand before that was implemented. (init scripts are left behind on package removal because they're considered configuration files.)
If removing these symlinks *doesn't* fix the problem, the issue may lie in one of the other scripts in /etc/rcS.d that are supposed to be there but are misbehaving nevertheless.
Note that the final versions of both the console-common and console-tools packages include checks for console-setup, and if present their init scripts are supposed to be no-ops. So if disabling the rcS symlinks for these fixes the problem for you, it's possible that you had removed these packages by hand before that was implemented. (init scripts are left behind on package removal because they're considered configuration files.)
If removing these symlinks *doesn't* fix the problem, the issue may lie in one of the other scripts in /etc/rcS.d that are supposed to be there but are misbehaving nevertheless.