I have same problems when saving in CS5, looks like you use CS 3 but problem is absolutely same. I tried to discuss it with SS and then it worked well for short time (they wrote "problem solved - no more glitches") but it's same again. Unfortunately the only way that works for me reliably is opening file in old AI10 software, copy image to blank document and save.
I think that there is something wrong in scripting of eps that says to their system that file is wrong.
I know absolutely nothing about script but this "%ADOBeginClientInjection: DocumentHeader "AI11EPS"" looks strange to me.