I've seen this a couple of times. I add a reporting snapshot to a managed package, and when the package gets installed, one or more of the field mappings are missing. Rest of the snapshot is there, just mappings completely absent.
I'm deploying the source report and the target object along w/ the snapshot, so everything it needs is in the package. And I'm able to set the mappings by editing the snapshot after the install. So there's nothing I can think of that should be preventing it.
Anyone seen this? There's nothing about it in the docs that I can find.
Did find this, but wouldn't expect an ANT problem to occur w/ the native package install process: https://success.salesforce.com/issues_view?id=a1p300000008Y5zAAE