In Subversion plugin version 1.39.

If a commit is made to an unpinned subversion external during a matrix build any child builds still in the queue will use the head version rather than the child jobs have significantly different sources.

To reproduce:

On a Jenkins install with 1 executor...
Create a matrix job with 1 axis containing 2 values
Select a subversion SCM pointing to a repository using unpinned externals
Add a build step which waits for a couple of minutes
Trigger a build
While the first configuration is building make a commit to the external