I have the same problems with cross-blog functions, if i activate the W3 Total Cache plugin in my WP multisite, but i think i have spotted the problem (i hope).
The problem is in object cache. So this is what i do. i enable the page cache, minify, database cache, browser cache (or any cache feature u want) but not the Object Cache, and then i delete wp-content/object-cache.php (i dont need it since i disable it). The plugin now working like a charm. The cross-blog functions like get_blog_permalink(), get_home_url(), get_blog_option() works fine.
But actually i really want the object cache works too, since it will greatly increase my site performance.
Frederick, i hope you find the best solution for us.
This is a great plugin.
