I've just experienced a problem with "Find Usages" and "Find Usages Advanced" in that it did not find a fairly obvious usage of a class within the solution. I quit VS2008 and deleted the _Resharper folders and then reopend the solution, then tried again, and it found several usages.
The class was public sealed in one project, and it was being referenced by a unit test in another project (that had a project reference within the same solution). THe solution is pretty large in that there are about 51 C# projects within it.
I'd love to figure out how I could repro this so I could give you more information.
I'm using R# 3.1.584.3 on VS2008, Windows Server 2003 R2 (x64).