I've been have this problem for awhile and haven't found a reason why it happens. Our installer uses an xml that sets the $CHOSEN_INSTALL_FEATURE_LIST$ and $CHOSEN_FEATURE_LIST$ variables based on the xml elements that are read in. The plugin that reads this xml is placed in the pre-install phase of the installation. I've put debugs print statements to see what the value is, and it does contain the correct feature short names. I know that in the documentation for these two variables it says that "IA will interpret the string value of these variable and discard values that do not make sense". But the thing is most of the time the install is successful. I've seen it consistently happen when I change the install location of the application from the default one. I can't pin point the other scenarios where this happens.
