Instead of self-extracting zips, you might try third-party zip libraries such as DynaZip. Under program control, you can do all the things you can do with the command line. We use this to give the user a backup facility inside of the program, as well as to install empty data when the user first installs the program (we found that users have an annoying tendency to reinstall over there data that has accumulated over a three-year period and which they never backed up, so we removed the data from the installation and instead install it the first time they run the program).

Hope this helps!

Jack