As in the answer of Escobar Ceaser, I suggest to use quotes arround the whole path. It's the common way to wrap the whole path in "", not only separate directory names within the path.
I had a similar issue that it didn't work for me. But it was no option to use "" within the path for separate directory names because the path contained environment variables, which theirself cover more than one directory hierarchies. The conclusion was that I missed the space between the closing " and the (
The correct version, with the space before the bracket, would be
If NOT exist "C:\Documents and Settings\John\Start Menu\Programs\Software Folder" (
start "\\filer\repo\lab\software\myapp\setup.exe"
pause
)