Multisite cannot find module in sites/default I haven recently set up a multisite setup with Live, staging and tag as the domina/subdomains used by the code 

in the sites directory I have the modules set up like so:

sites/all/modules/&lt;modules shared by ALL sites&gt;
sites/default/modules/&lt;modules ONLY used by default&gt;
sites/tag.example.com/modules/&lt;modules ONLY used by tag&gt;
sites/staging.example.com/modules/&lt;modules ONLY used by staging&gt;


in the default, staging and tag modules directory are independent copies of modules that I am developing.

However when I add new urls to hook_menu() in any module in staging it is not picked up at all, only when the function is populated to sites/all

further to this, the modules disappear from the admin/modules page

on top of this there is this next issue.

If I place My_Module into the default and staging folder there are times that it either says that a function name cannot be found (when it is blatantly using the module) OR even worse is when it says I cannot re-declare a given function name 

So can anyone point out if I am doing something wrong?

Am I putting the modules in the correct places because when I have EXACT duplicates of a module in separate site folders (staging and default but not all)  I am able to edit the content and see that the content has been edited but not add new urls/functions that get picked up.

And YES I am flushing all caches when uploading new hook_menu() items and function changes etc

Any Help is appreciated.

Thanks, Jim.
So this was the issue,

When I created the sub-domain i used cpanel, even though I specified

/home/&lt;username&gt;/&lt;subdomain-name&gt;

as the home directory path,

it would override it in the vhost entry to: 

/home/&lt;username&gt;/public_html/&lt;subdomain-name&gt;

so,  even though I created the symlink at the right place, it never hit it, 
so when I went to the subdomain url is was picked up by the drupal htaccess as a url to the live site

lots of confusion and lots of annoying behaviours

As soon as I edited the vhost entry to the corect path, everything worked correctly

thanks for all the reads though

Jim