I have specified a list of applications as our default selection for deployments in the customsettings.ini file. There are instances where we would want to deselect some of those applications at the "Select Applications" dialog of the PSDWizard. These changes do not appear to be respected, and all the applications specified in the customsettings.ini are still installed, even after being deselected.
I've attached the initial "Selection Applications" dialog window, "Summary details" dialog window, redacted customsettings.ini, and a redacted PSDApplicaitons.log file from a test deployment.
customsettings-redacted.txt
PSDApplications-Redacted.log