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@jglick, sorry I lost you with my comments and am not doing a good job of watching this thread. Here is the bottom line from what I can tell:
As the stacktrace shows, the problem is that b.checkouts is null on line 419 (here). (Note this seem to have moved to around line 423 on master).
I have identified two different build.xml files for the same job wherein for the one, when it hits this line, checkouts is non-null and for the other when it hits, checkouts is null. I am hoping that you can feed these two attached files into Jenkins' deserializer and figure out why the one is yielding a null checkout property when the other does not. As I recall the first file ...-build.xml is the one that yeilds the null value and ...-build-1.xml is the one that works as expected.
Hope that helps.