We have set up two websites in IIS, each under different Application pools. They point the same codebase. The sites in EPiServer.config are set up with different start page ids and this is evident through the edit mode interface. However, whenever trying to access the 'second site', I am directed to the home page of the first website, which is default.aspx in root directory.
Any help on this, is much appreciated.
After several days of head scratching, I found the answer. The settings in EPiServerFramework.config needed to be manually modified to match sites on EPiServer.config