I cleaned up the command line arguments and got rid of the arguments list that you were using in favor of the built in my.application.commandlineargs.
change option compare to text from binary so that the command line arguments could be case-insensitive
Converted command line argument parsing from multiple If statements to a select-case statement, and added a case else, for unknown command line arguments.
Added some syntax checking
Noticed that updatedefs was not working when the app was hidden, due to the fact that it was using a windows form backgroundworker to keep track of progress etc.
I changed it to use webclient for the silent mode so that it would work when hidden.
broke out the file download function from the button click, since button clicks don’t work when the form is hidden.
All primary command line options now work with silent mode, and Javara is now fully scriptable.