Nor does the build timeout seem to apply if the build fails to even start, e.g. if the target node is offline.

I'm seeing a similar problem for matrix jobs with build timeout set. I've seen one case where a matrix job with a 2x2 configuration times out, but the configurations appear to keep going and cannot be stopped. At the bottom of the console output for each configuration, I see the "Build timed out (after 120 minutes). Marking the build as aborted." entries in the logs, but the spinner at the bottom is still moving and each of the configuration jobs appear to keep trying to execute. I tried to stop each configuration build the normal way (clicking the red X), which didn't work after multiple attempts, so I looked at the threads via the JavaMelody Monitoring plugin and all 4 of them are in RUNNABLE state. Trying to kill each thread does not work either, so I'm stuck here with the only choice of restarting Jenkins.

Could not reproduce in my environment.
Build timeout does not (and can not) start its timer for matrix parents.
Please report detailed steps to reproduce the problem, and attach log files.
(Especially I want versions of Jenkins and plugins)

This ticket will be closed in a month if no more reports.

I've just seen this issue too.  In our case, we run a multi-configuration job to sync git reference repos across multiple slaves.  When one of those slaves is inaccessible (offline because it ran out of disk space for example) then the multi-config job hangs waiting to connect with that slave and does not time out after an absolute limit.

Sorry, I'm not sure which versions of Jenkins and plugins we're using because I don't have admin access.

Please attach the console log.
And I also want to know the configuration of your job, especially what you mean with "sync git reference repos across multiple slaves", as build-timeout doesn't work while the SCM phase.