Have you checked the IIS logs to see if they are hitting a specific page and injecting it there?
Do you load any data from a database? You could check in the tables and see if anything out of the ordinary appears there.
It is unlikely that the .aspx pages have actually been physically modified and even more unlikely that the DLL have been as .aspx.cs files are compiled in to your BIN folder as DLL's. The more likely scenario is that you have an unsecure page that a malicious site is injecting its script into. The other possible attack vector is that you have had malicious code via SQL injection and are loading it each time.