I'm using the NAVT plugin (version 1.0.26) with WordPress MU (version 2.6.1).
NAVT contains the following line of code:
add_option($key, $value, $description, 'no');
Later in the code, it calls get_option and doesn't get anything back. If I change the above line to this it works fine:
add_option($key, $value, $description, 'yes');
From what I can tell, there doesn't seem to be anything that gets options from the database that aren't autoloaded at the initialization of wordpress. I would think it would be in the wp_load_alloptions() function because that's where wp_cache_set() is called in that file. All it has in there is a query that searches only for autoloaded options and if doesn't find any, it grabs all options. It doesn't seem to handle the case where there are some autoloaded options and some that should be loaded later.
I'm not terribly well versed in wordpress code, so I might be way off on this. Also, I'm not sure if it's a WordPress or WordPress MU problem. It doesn't seem to be a NAVT problem though.
If anyone has any thoughts on this I'd love to hear them!