I have found that editing the Theme/Image[@ImageFile] value to anything other than Logo.png with cause the described error.
Changing the value back to Logo.png reverses the error.
Setting the value in Wix/Bundle/bal:WixStandardBootstrapperApplication[@LogoFile] appropriately changes the image and does not cause the setup.exe to produce an error.
Note I downloaded and used the default theme for HyperlinkLicense for my custom template with only change being the ImageFile attribute. It is improbable that this was a result of ill-formed xml.