I have actually had an upgrade on a Shuttle segment confirmed at the time of booking, well in advance of the 100 hour window. When purchasing the itinerary, the 1K agent assigned me seats in F on all 3 segments (using miles on the 2 regular segments and the comp upgrade for 1Ks on the Shuttle segment). It surprised me at the time, as I was expecting the comp Shuttle upgrade to be treated exactly like a regular 500-mile upgrade request.

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Tony