I recently happened to help a few customers resolve an issue with Helicon ISAPI URL Rewrite module when Sitecore runs in Integrated mode. So, I decided to make create a quick post about it as it took me awhile to figure out why this was happening. I even had to contact Helicon support channel to see if they had any insights into this issue.
The long story short Helicon module has to be configured in early request processing in order to work with Sitecore in Integrated pipeline mode. Here is the setting that you need to set up to make it happen: http://www.helicontech.com/isapi_rewrite/doc/NotificationType.htm
Now a few more details for those who still reading. So, why this becomes an issue when you run your Sitecore app in Integrated mode? The answer lies in the model that Integrated pipeline has. It’s different from Classic mode (aka IIS 6 model) which is based around ISAPI modules. For those who want to dive into details I’d recommend to read these articles: ASP.NET Application Life Cycle Overview for IIS 7.0 and Comparing Native-Code and Managed-Code Notifications [IIS 7].
As all native and managed modules can subscribe to the same processing events when you run you app in integrated mode, the Helicon ISAPI module turns out to be not the first one that accepts a request. The first event that gets raised is Authentication one. Sitecore Http Module gets subscribed to that event thus it’s the first one who intercepts the request. After the Http Module the request gets changed and it points to the physical file, which is a physical layout page for your dynamically constructed page represented by a Sitecore item. As a result Helicon module gets a “wrong” URL.
If you’re not satisfied with this workaround, consider using official Microsoft URL Rewrite module.
For those who are still looking for the solution it's a first link in this post 
Hope this will save someone a bit of time.
