I have actually run into that issue, but it was more to do with encountering a "corrupt" MXD (I put corrupt in quotes since MXD Doctor found no corrupted items, but once I ran a fix with MXD Doctor it worked fine, so I would call that corrupted). I am not sure what was wrong with it since it opened with ArcMap fine, just with broken links. Running through MXD Doctor showed a bunch of strange modules that were removed when I ran a fix and it processed fine after that. I've mostly seen this behaviour from some v10 .mxd files that were converted from prior version .mxt files, but that may be anecdotal. Not sure if this would be related to your situation or not. When I batched through I fixed about 500 mxds that ran fine once the "corrupted" ones were fixed or removed.