The profiler starts the executable you supply using Process.Start and some extra environment variables that tell .NET to load the profiler and which process to attach to. Provided the variables aren't unset, the profiler will be loaded into the CLR whenever it starts (even if it's in a process launched by the one you initially specify)
Can you give more details about how the addin doesn't work? If it fails to load, then it's probably something to do with the way Excel is being started. If Excel crashes when you try to use it, there's a good chance that you've found a bug in the profiler core. If it works but doesn't profile, the chances are that the variables have got cleared somehow before the add-in started, or the profiler didn't load for some reason (unfortunately, this is the hardest kind of problem to narrow down, as there's little feedback from .NET on what happened).
Older versions of the profiler did have some issues with Excel - specifically to do with Data Execution Prevention - they would crash when you took a snapshot, though profiling would work OK otherwise. This should have been fixed in version 7.1, however, so I'm interested if this still occurs in newer versions.
Red Gate Software Ltd.