Yes, by default the monitor use the version number of the assembly, using Assembly.GetEntryAssembly() as the first choice and Assembly.GetCallingAssembly() it the former returns null.
But it's possible to report any version number you want: simply create the monitor with settings and in those settings specify the desired version number. Like so:
var settings = AnalyticsMonitorFactory.CreateSettings(ProductID);
settings.Version = new Version(1, 2, 3, 4);
var monitor = AnalyticsMonitorFactory.CreateMonitor(settings);
I'm not certain about the specifics of retrieving the version number in a ClickOnce scenario like yours, but I'd be happy to hear about how you solve it so we can start a "best practices" for ClickOnce deployed applications.
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