Edit: Damn, I should really learn to refresh posts before replying ;) I'll leave my comments up as they show others how this can occur.
Hi, when I look at the file in OmniGraffle 5 Pro, the reason is that the offsets are different with object 1 settings as in the picture below and object 2 settings at 100% (the
Use default offsets is checked):
That would explain why it is occurring but from your screenshots it appears that you are using version 4 of OmniGraffle so I don't know how you would have made these settings yourself? Is it from a file sent to you by another user?