Smss.exe (Session Manager) is absolutely integral in creating new user sessions, including Terminal Services sessions when people log on remotely.
When Smss starts, it checks whether it is the first instance (the
master Smss) or an instance of itself that the master Smss launched to
create a session.
According to Mark Russinovich's Windows Internals book, Smss.exe includes algorithms that make use of processor affinity in a special way:
"By creating multiple instances of itself during boot-up and Terminal
Services session creation, Smss can create multiple sessions at the
same time (at maximum, four concurrent sessions, plus one more for
each extra CPU beyond one)."
And:
If the system supports hot processor add, enables automatic processor
affinity updates so that if new processors are added new sessions will
take advantage of the new processors.
Your tweaking of the process's affinity mask is likely interfering with those algorithms.
So in short, don't do that. Whatever you're trying to accomplish, you're very likely going about it in the wrong way.