You're right Mark, I suspect the file is in a different folder too... but perhaps for a different reason than you might expect. The hint I think is that he saved maps under the Mapper8 directory.
Jerrod - you didnt mention which version of Windows you are running, but if its Vista or 7, I suspect whats happening is you have discovered the wonders of Microsoft's wonderfully esoteric Virtual Store
Basically, you say you made a folder under the Mapper8 directory. But in Vista & 7, you arent supposed to write files into the Program Files directory structure. So what Windows does when you save a file into that structure is move it to a 'virtual store', or basically a different directory that acts as an alias for the Program Files path. This way original files in that directory structure cant be overwritten (by malware, for example). If you try to open a file that resides in the Program Files within an application, Windows first looks in the Virtual Store to see if there is a file there that was originally saved into the Program Files directory, and opens that. Thats why in Windows Explorer, the file isnt there... but in the application, if you access that specific file, it finds it.
This isnt an FM issue - its Windows doing what its supposed to be doing. What I'd recommend is saving your maps into either a folder under the 'My Documents' folder, or some other folder that does not reside in the Program Files structure.
Of course, if you arent running Vista/7, then thats not it, and you just read a nice description of a little known Windows feature that doesnt apply to you.