In the Domino for Microsoft IIS configuration, all URL requests received by IIS that contain the letters ".nsf" are passed to Domino. However, it is possible to use a Domino replication ID to identify a Domino page which does not include the letters ".nsf" in the URL syntax, and thus would not be passed to Domino in the default configuration. Note that Domain Search uses replication IDs when returning results as well.
If you are using Domino for IIS you should fill out the "Generating References to this Server" section under Internet Protocols / Domino Web Engine in the Server document in your Domino Directory. This indicates you are using IIS (and therefore require the .nsf in your URL syntax), and allows you to specify how IIS is configured so references to this server can be properly generated.
Setting the "Does this server use IIS?" field to Yes replaces the use of the DominoGenR5RepIdSyntax=1 setting in your notes.ini as previously suggested in R5.0 documentation.
When IIS is indicated, the Domino server will add the string ".nsf" to all Domino-generated URLs using the following syntax, which enables the IIS filter to pass the request to Domino:
http://server/__replication id.nsf/?Command
...where "replication id" is the 16 digit identity of the database prefixed with 2 underscores. For example:
http://www.lotus.com/__852559DF0070D6E7.nsf/?OpenDatabase
The URLs that use this syntax includes those produced in a page that is a result of a Domain Search. Domino R5 servers process the page as it would normally. Domino 4.x servers do not recognize these URLs.
If you are upgrading a 4.x Web site that includes explicit URLs using replication IDs, and you want to run it in a Domino for IIS configuration, you need to manually change the URLs to match the syntax above.