We've encountered similar problem after Jenkins crash.
We're using multi-dimension matrix jobs, and one of our matrix configurations stopped working.
I've found that affected job's matrix configuration persisting in <JENKINS HOME>/jobs/<Matrix JOB>/configurations/axis-<A>/<Value A>/axis-<B>/<Value B>/config.xml "disabled" element value left with value true.
<disabled>true</disabled>
After changing it's value to false, and reloading Jenkins configuration (Reload Configuration from Disk or restart Jenkins) my matrix job has started working.

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