Multiple WordPress Installations in the Same Account

I have been trying to resolve a problem I have been having with wordpress. I think I now know the source of the problem but don’t know how to solve it.

I have several wordpress installations in my hosting account with GoDaddy. The Account is windows based. The WordPress installations were all installed into sub-direct directories of that account (e.g innovy.com/canadarent2own). I recently setup wordpress in the root of the account innovalty.com. Now none of my other wordpress installations are working .. the ones in the sub-directories. However, when i change my permalinks to the Default and not use the Pretty links, the site will work. This is not a viable solution for me since I have a lot of links hard coded.

I have tried several changes related to “Home URL”, “Site URL”, “web.config”, and some other stuff but it didn’t seem to fix the problem. I’m sure I’m missing some steps.

Does anyone know what needs to be done to fix the problem? And no I don’t want to move to a Linux server.