At least on the T400, if you close the lid while the system is shutting down - then it just ends up rebooting.
Initially thought it was a kernel issue, but managed to replicate it with an LTS kernel that didn't have this problem before updating from the testing release.
Moreover, dmesg shows nothing that could be indicative.
Note that if the lid remains open then the system shuts down normally, the issue arises only when trying to shut down and subsequently close the lid before the system has actually powered off (even if the screen is already blank).
Doesn't make a difference if plugged in/on battery or even plugged in without batteries installed.
I still am not 100% sure of this, but it seems to be an issue related to WoL.
Adding a udev rule to disable WoL on all adapters (802.3 and 802.11) seems to solve the problem.