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Yes, I have other project types that were affected. It was not 100% universal- some of the other jobs kept one or two builds in history (out of many), but the matrix jobs and the jobs related to them (upstream) lost everything.
I went ahead and upgraded to the new version of Jenkins and the matrix plugin. The history was completely gone again this morning with 1.563 Jenkins and 1.2 Matrix plugin.
I realized that my builds and workspace directory for the masters config.xml were set to non-standard locations. I changed them to match my other Jenkins server and am hoping that this may clear up the issue.