Doesn't appear to be detecting your previous install:

[186C:1C04][2014-03-07T14:57:34]i101: Detected package: MyApplication1,
state: Absent, cached: None 
[186C:1C04][2014-03-07T14:57:34]i101: Detected package: MyApplication2,
state: Absent, cached: None 

It says that its current state is "Absent", as in, it didn't find an
existing install. Hmm...in your custom bootstrapper's DetectPackageComplete
method, are you looking for the name of your MSI, such as:

protected void DetectPackageComplete(object sender,
DetectPackageCompleteEventArgs e)
{
  if (e.PackageId.Equals("MyApplication1.msi", StringComparison.Ordinal))
  {
    // assuming you've set up an InstallState enum like the WiX bootstrapper
has...
    this.State = e.State == PackageState.Present ? InstallState.Present :
InstallState.NotPresent;
  }
}





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