On the main composer.json I have:

"include": [ "composer.root.json" ],

On composer.root.json I have:

"autoload": { "files": ["private/bootstrap.php"] }

When I run composer update I get this entry on vendor/composer/autoload_files.php:

return array( ... $baseDir . '/cprivate/bootstrap.php', );

The prepended c seems to come from the included composer.root.json's file name.
If I change the composer.json's include section to:

"include": [ "./composer.root.json" ],

I get a correct result.
I see this plugin prepends the relative path of each included composer.json file to paths specified on that file's autoload.files section, so this is probably a bug on the algorithm that generates that prefix path.