It was a Windows 7 issue.

Windows 7 is saving my maps to a second location apart from the saving Worldcrafdt does, in c:\users\myusername\appdata\local\virtualstore\program files\worldcraft\, apart from c:\program files\worldcraft\maps\ that Worldcraft saves to by default.

This doesn't happen all the time, so there is two different versions, and sometimes it loads the WC version and others the second version, leading to me thinking that it wasn't saving them half the time.

This never happened to me in Windows 95/98 SE/2000/XP sp2 and sp3 and in Ubuntu, Fedora and Red Hat distros. 

Not a justification mind...just what's happening there!

The "Program Files" folder is regarded by the microsoft team as a place you should fear to tread. The average user shouldn't need to ever look in the folders there, and because all the stuff in there is executable, it's security sensitive and unprivileged processes aren't allowed to make changes. Previous versions of windows did not enforce this, but Windows 7 (and vista maybe) make the folders protected.

Now, lots of old programs regard their program files folder as something they can write to at will, which causes a compatibility problem when you try in a newer OS. What Windows 7 attempts is to detect when that's happening, and redirect all the file activity elsewhere - to a lower security folder where you have permission to write things but can't do damage. This redirection is meant to be transparent to the program receiving the workaround.

Worldcraft is a pretty old program, certainly not designed at a time when these rules were enforced in this way. So saving maps in the program directory triggers the compatibility stuff, but evidently it's not working 100%. My advice is to move the folder out of Program Files, to it's own folder off the hard drive. You might also need to reset the permissions on the folder once it arrive. This also lets you have a shorter path without spaces, which can be helpful at the compiling stages : -) 

Did not know about the folder redirection. Very interesting and good to know. 

to the big list of those i use regularly that work badly on Windows xp sp3/vista/7/8. At least it hasn't gone to the also big list of those that i have to tweak to deactivate Windows unfounded complains (mainly at installing) or those that directly don't work at all.

Thanks a lot for the info, Preach, very instructive, and thanks to you i can now map a bit in this computer. Never suspected something like that happened, even though that now that i think it well, Windows 7 is full of occasions where it tries to restrict what you do. I hope that i won't be forced to switch to Windows 7 in a loooong time.