TortoiseCVS looks at the line endings of the CVS/Root file. This file is created when the module is first checked out, and is usually not changed afterwards. So when you check the UNIX line endings checkbox in the Checkout dialog, CVS creates the Root file with UNIX line endings, and this again causes TortoiseCVS to force CVS to use UNIX line endings on all subsequent CVS operations.

See also Sandbox DOS/UNIX preference setting.