The question is too old, but I run in the same issue.
Anirudh Ramanathan's answer is correct.
The solution is to add new Application in different ApplicationPools.
Right from Microsoft's documentation:
In the Connections pane, expand the Sites node.
Right-click the site for which you want to create an application, and click Add Application.
In the Alias text box, type a value for the application URL, such as marketing. This value is used to access the application in a URL.
Click Select if you want to select a different application pool than the one listed in the Application pool box. In the Select Application Pool dialog box, select an application pool from the Application pool list and then click OK.
In the Physical path text box, type the physical path of the application's folder, or click the browse button (...) to navigate the file system to find the folder.
Optionally, click Connect as to specify credentials that have permission to access the physical path. If you do not use specific credentials, select the Application user (pass-through authentication) option on the >Connect As dialog box.
Optionally, click Test Settings to verify the settings that you specified for the application.
Click OK.
Complete documentation here
N.B.: "click Test Settings to verify the settings that you specified for the application" may produce an error. According to other SO answers, it seems to be a bug. I ignore this alert and everything run well.