I just had to debug an issue where Asp.Net seemed to be caching the dll's of projects referenced by the website, even after those were rebuilt
The solution compiles, but at runtime Asp.Net references an out of date binary in C:\Windows\Microsoft.NET\Framework\v4.0.30319\Temporary ASP.NET Files\root, and throws an exception. (I don't think the specific exception is relevant, its simply the fact that the underlying code is old, in my case its an issue with LLBLGEN where entity indexes are out of whack)
This is a new issue, but seems to be happening consistently across development workstations, and our integration server, so I think it must be some configuration we have.
We are developing against Asp.Net 4, on IIS 7.5
Update
We are using the optimizeCompilations flag on system.web/compilation element in web.config. I can't see how this might affect it, but will flip this and see if anything changes.