When packager generates msi package on windows 7 platform sometimes created msi doesn't delete itself. So, the command msiexec /i HelloWorld-1.0.msi /quiet correctly install it, then msiexec /x HelloWorld-1.0.msi /quiet don't delete it correctly: all files in %LOCALAPPDATA% is untouched.

I attach HelloWorld project. You can create package by javafxpackager by invoking this:
ant -f simple-build-cli.xml deploy-all
If you want to compare this result to ant tool result (which is correct) you can invoke this:
ant -f simple-build.xml deploy-all