Hey kobus, thanks for your reply. I really appreciate it. However, I've already done what you asked me to do but each time i tried to run my application from the shortcut, the "Start In" would only have "C:\projects" which is my $INSTDIR. It dosent seem to read anything after my $INSTDIR.
Eg: CreateShortCut "$DESKTOP\SMSCenter.lnk" "$INSTDIR\SMSCenter\bin\startup.bat"
It will not register "SMSCenter\bin\". It only recognises $INSTDIR and only registers that as my "Start In". I need my Start In to be in the bin folder because that's where my batch file is located. I hope this is clearer now