What's the difference between the following cmd scripts?

Start Chrome

This one works, because Chrome's executable is located in a folder which is in the PATH environment variable. start looks for programs in all folders in that variable. The environment variable PATHEXT contains a list of file extensions to look for and as .exe is contained by default, you don't need to write chrome.exe.

start "FOO_DIR\FOO.exe"

This does not work, because start will use its first argument as the window title if it is quoted. So this will open a new CMD with "FOO_DIR\FOO.exe" as its title.

To circumvent this, you can simply add an empty title argument before your command:

start "" "FOO_DIR\FOO.exe"

Try adding "title" or at least "" after start like this:

start "title" "FOO_DIR\FOO.exe"

or

start "title" /B  "FOO_DIR\FOO.exe"

The root cause of the problem is that first argument in "" quotes is interpreted as a title parameter for new cmd window.

Also it helps to look at the command reference (link)