When using Shell it will execute the file in the current directory unless specified. As far as I know, so don't add the path to the filename you execute and you should be fine... See code below

Private Sub CmdRun_Click()
Dim AppName as String
Dim AppProcID as Integer

AppName = "MyApp.exe"

On Error Goto ErrRoutine
AppProcID = Shell(AppName)
Exit Sub

ErrRoutine:
'exe wasn't found or some internal error occured
'you can either, log it to a file, message box it or
'ignore it. if you run this code from the VB IDE without
'making this app an .exe Shell command will assume MyApp.exe
'is in the current dir for VB. example: c:\program files\DevStudio\VisualBasic\MyApp.exe
End Sub