The component guid is mentioned once more later in the log but the entries are almost identical for both attempts:
MSI (s) (34:F4) [08:34:45:812]: Executing op: RegisterSharedComponentProvider(PatchGUID={66911576-86A6-4A9C-AF86-9370E40E09EA},MediaCabinet=#PCW_CAB_LnchApps,File=MyApp.exe,Component={B02BFA02-FEBE-4965-A07A-0150C44CDA7C},ComponentVersion=1.0.0.0,ProductCode={33250B4C-B2D2-4F36-AB12-D5FF0757C973},ProductVersion=6.13.7604,PatchSize=554,PatchAttributes=0,PatchSequence=10006,SharedComponent=0,IsFullFile=0
MSI (s) (34:50) [08:37:24:238]: Executing op: FileCopy(SourceName=MyApp.exe,SourceCabKey=MyApp.exe,DestName=MyApp.exe,Attributes=0,FileSize=422400,PerTick=65536,,VerifyMedia=1,,TotalPatches=1,,,CheckCRC=0,Version=1.0.0.0,Language=0,InstallMode=327680000,,,,,,,)
MSI (s) (34:50) [08:37:24:242]: File: C:\Program Files (x86)\MyCompany\MyApplication\MyApp.exe; Patch targets existing file.; Smart patch; Existing file is of an equal version
... the only difference being "InstallMode" - it's 327417856 in the quiet attempt and 327680000 in the successful attempt.
But wait!
In the quiet mode log, I found this:
MSI (s) (64:0C) [09:05:12:910]: Executing op: CacheBaselineFile(Baseline=0,FileKey=MyApp.exe,FilePath=C:\Program Files (x86)\MyCompany\MyApplication\MyApp.exe,,Existing=0)
MSI (s) (64:0C) [09:05:12:911]: Executing op: PatchApply(PatchName=MyApp.exe,TargetName=C:\Program Files (x86)\MyCompany\MyApplication\MyApp.exe,PatchSize=554,TargetSize=422400,PerTick=0,,FileAttributes=0,PatchAttributes=0,CheckCRC=0)
MSI (s) (64:0C) [09:05:12:912]: Skipping all patches for file 'C:\Program Files (x86)\MyCompany\MyApplication\MyApp.exe'. File does not need to be patched.