I've already searched the KB as well. I've tried giving the project a different ProductID since I suspected some kind of confusion with the CompID codes. I also see this in the MSI log
Action start 7:51:51: CostFinalize.
MSI © (64:94): Note: 1: 2262 2: Patch 3: -2147287038
Which seems to say a 'Patch' stream doesn't exist? Any ideas?