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Same issue, OmniGraffle Pro 5.3.4 on OS X 10.7.1. Here is my AppleScript, as basic as possible:

Code:
tell application "OmniGraffle Professional 5"
	open "Bengal:Users:gene:Desktop:Test.graffle"
end tell
OmniGraffle opens the file just fine, but the AppleScript never gets control back. Clicking Stop in the Script Editor does nothing. Actually quitting OmniGraffle pops up this error in Script Editor:

Code:
error "OmniGraffle Professional 5 got an error: Connection is invalid." number -609
I've tried completely deleting OmniGraffle (including Preference files etc.) and reinstalling with no change in behaviour. I've tried a few different test files, including a completely blank one and one with just a single square shape. Same results.

This worked fine until (I believe) I upgraded to Lion. I've tried switching off Resume functionality in System Preferences > General to no effect.

I would love a workaround for this, or even some indication about whether others are seeing this problem.