I have what for me at least is a really strange situation and would very much appreciate any help in finding a solution.
I have a primary site (primary domain.com) which has been in operation for a number of years. This primary site also supports a related blog (primary site/blog) and both blog and primary site function without problem. Obviously the primary site is located in the root (public_html) directory with the blog being located in a sub-directory simply named "Blog"
Several weeks ago I added an add-on domain (add-on domain.com) with the site files being located in its own sub-directory off the root
directory. The add-on domain has been functioning as it should for several weeks. As a part of the development of the site I tried to add a related blog in a sub-directory off the add-on directory. I.e root directory/add-on site/add-on site blog/, this is where all the problems commenced.
The problem is as follows - having installed wordpress 3.3.1 generally the basic blog appears to function and load ok. After several hours I get a 404 page not found error for the add-on domain and subsequently the related blog.
If I effectively deactivate the blog by renaming the blog directory "old add-on blog the add-on site will once again load but only after several hours (normally after I have slept for the night) but not immediately. I have replicated this situation several times in my efforts to resolve this issue, but thus far have not managed to find a solution. This leads me to believe that the problem is in some way related to something the host server resets daily but I have no idea what, nor how to find a solution.
I have searched a variety of forums etc. but have yet to find anything even close to this problem so I remain totally baffled.
All help or advice in resolving this issue will be very much appreciated.