start.command permission denied even after chmod
If you actually used chmod x+u filename then here is the results of a sample from Terminal:

$ echo 'echo Hello World!' &gt; hello.command
$ ls -l hello.command
-rw-r--r--  1 user  staff  18 Aug  5 14:24 hello.command
$ chmod x+u hello.command
chmod: Invalid file mode: x+u
$ ./hello.command
-bash: ./hello.command: Permission denied
$ chmod +x hello.command
$ ls -l hello.command
-rwxr-xr-x  1 user  staff  18 Aug  5 14:24 hello.command
$ ./hello.command
Hello World!
$ 


It just needs to be: chmod +x filename

If you only want it executable for the User, then use: chmod u+x filename