Just got an OTA update on my Nexus One for Gingerbread 2.3.6. Reboot to install. Oops, what's that? Lost my root. No problem. Reboot into recovery and reinstalled su.zip. Oops, what's that again? Link2SD gave a mount warning and requested a quick reboot. After the quick reboot, the warning was gone and all linked apps were working well, but I don't relish having to reboot twice every time from now on! After some mucking around, here's how to fix it. I had to uninstall Link2SD, reinstall it, run and select the filesystem type of the second partition, then reboot. This reinstalls the mount script correctly in the new ROM and everything works fine after that.