It's happened to me on several occasions over several different reboots.  I don't know if I remember it happening right after I first installed the SCP, but I'm pretty sure it didn't.  Just to make sure we're on the same page:  the error is occurring with the original, vanilla, Volition release of Fred 2.  I have 3 versions of Fred_Open installed in the same directory:  one for Inferno, the 3.5.5 version, and a recent HTL release.  I also have the VP files for the Freespace Port in the same directory.  My initial thought was that one of the above was simply interfering with the original Fred2; I can't see how it can be a memory leak, since that program hasn't been changed in any way with the installation of SCP.
The error message doesn't really say anything; it's the standard XP window when a program has an unexpected error, asking if I want to send the error data to Microsoft or not.  There is a link to get more technical information about the error report, but it's just miles worth of code that probably doesn't do anyone any good 

.
Edit:  I haven't yet tried moving all of the SCP stuff out of the FS2 directory, mainly because I've been too lazy 

.  I'll give it a shot tomorrow, though.  I'm also aware that simply uninstalling everything FS2-related and reinstalling without the SCP will fix the problem, but it's not worth the effort.