I just tried a tiny test program in BlitzMax 1.22 (haven't updated yet):
CopyFile "1.txt", "2.txt"
with MoleBox Pro 2.5.12 (just noticed that I need to update this, too <g>). I tried this once where "1.txt" was in the same folder as the MoleBoxed .exe but wasn't included in its archive, and once where it was included in the package but wasn't in the folder outside the package. CopyFile created a copied "2.txt" both times.
I then tried the same program in Blitz3D 1.98 and it worked with "1.txt" in the folder but
not where it was packed instead of in the archive (which sounds like what you're describing).
I also tried using uppercase filenames (I once had problem with MoleBox converting ReadLine-ed text to all-uppercase, though that particular issue was fixed in a MoleBox update). It still didn't work in the B3D version, while it still worked in the BlitzMax version (and uppercased the copied filename correctly).
Neither using a separate data section nor changing "Make packed files visible for standard OpenFile dialog" made any difference in the B3D version. Neither did using a debug build in B3D.
So, it does look like while BlitzMax's CopyFile works with MoleBox, Blitz3D's version currently doesn't. If you contact March on the
http://devforum.teggo.com/viewforum.php?f=2 forum, they might be able to fix this with a MoleBox update like that which fixed my B3D uppercase text file problem.