I am able to successfully pass a SQL file from say ConText editor using its "Tools" facilities, not so from EmEditor.
Steps to repro:

1) Create and save a SQL file that encompasses code as

USE SandBoxDb;
GO

/* This is a test */
SELECT Top 1 *
FROM test;
GO
2) Configure a new tool to launch
C:\Program Files\Microsoft SQL Server\100\Tools\Binn\SQLCMD.EXE

See the rest of the setup in this image: http://www.box.com/s/6n28qruy38ehqvxnqt85

An attempt to run produces an error:

---------------------------
EmEditor
---------------------------
The directory name is invalid.

C:\Program Files\Microsoft SQL Server\100\Tools\Binn\SQLCMD.EXE
---------------------------
OK
---------------------------

Please note this directory is fine.

Hint: the spaces in the path cannot be tolerated.