I think if you escape the backslashes with backslashes, they should work.
$ssh->exec('cd E:\\\\Titan\\ Torque\\\\Jobs');
In a test:
echo 'E\\:a thing with\slashes\\';
echo "\n";
echo 'E\\\\:a thing with\\\\slashes\\';
gives
E\:a thing with\slashes\
E\\:a thing with\\slashes\
In case you're curious, the reason a single backslash works at all, is because \
isn't a special escape sequence so it's put into the resultant string literally.