I think your problem may be due to the fact that you specified repository directories inside the script editor.
Looking at the options for that, it appears that it is set by default to have the repository path as ".". You can't set it to nothing in the editor, and it appears your default is the bin\win32 folder. I didn't set it, so I'm blaming you for that.One question I have for you is in regards to handling multiple script files (because, obviously, packing everything into one gigantic script is stupid). Can the compiler be set up such that if a script includes a BSL file, it searches for an existing BVM. If the BVM's timestamp is older than the BSL's timestamp (or the BVM doesn't exist), the BSL is recompiled on the spot and the new BVM is included.
That would require the BSL to exist, so it could be handled such that in the case the BSL doesn't exist, the BVM is just used as-is. (And if neither exist, the compiler shakes its head and asks if you're insane.)
The way it is now (as far as I've seen, since I haven't gone through the docs entirely), it seems that you have to have the host application check all the files and recompile them if necessary before actually loading the scripts. This isn't really convenient because it means that, as a solution, I still have to spend a lot of time including functionality that I think should be part of the compiler. It'd be like getting a vacuum cleaner, except it has no handle, so you tape a broom handle to it. Should have come with a handle, but instead you're forced into adding functionality to the vacuum in a way.
For example, BlitzMax will recompile imported source files if it has to, or just link to the objects that were already compiled (or compile them if the objects simply don't exist). What I'm more or less hoping for is something similar to this, if the above didn't make much sense.
And it looks like the end of the month timestamp-screwy just happened...