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The issue appears to boil down to the way changelist is being gathered via the git log command. That is happening in 'showRevision' method (CliGitAPIImpl.java):
git log --full-history --no-abbrev --format=raw -M -m --raw <oldSHA>..<newSha>
When the SHAs come from different branches, the result has more entries than expected, so 'isRevExcluded' method in GiSCM.java will check changes that were already built before.