One long-standing piece of flakiness in OmniGraffle's scripting of text properties is that the scripted change is sometimes only shown at other zoom levels - change the zoom and it become visible, return to the original zoom level and it vanishes.
(A backfiring of some attempt to economize on screen refresh events ?)
Hard to know whether this is a factor without seeing your script. But it might be worth adding a zoom level nudge at the end of it. (Subject to the caveat that things will initially still be amiss at the original zoom level).
Something like:
Code:
tell application id "OGfl"
tell front window to set zoom to (zoom * (0.999))
end tell
The most important thing, however, is to report this through OG
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