I don't understand. What do you mean by "pop up run the bat file."? Did it not run the batch file or only didn't pop up something? It is not supposed to pop up anything, it is supposed to copy any output from the batch file to the installer log. If the batch file doesn't have any output it won't nothing in the log. Did the batch file do his job or not?
A possible problem might be that the batch file assumes a certain current directory. The current directory of the installer is the directory in which it started. In the next version (that will hopefully come out tomorrow) there will be an option to change the current directory.
For now, if this is indeed the problem, you dynamically write the batch file from NSIS using FileOpen, FileWrite and FileClose.
But first try to give the batch file a .bat extension. Use:
GetTempFileName $0
Delete $0
StrCpy $0 "$0.bat"
File /oname=$0 mybatch.bat
nsExec::ExecToLog $0
Delete $0
Instead of the code above.