Offhand I'm not sure I've ever heard of this on Windows. Under UNIX, it could be caused by having one set of files with lower case names and one with upper case names (since the OS considers case significant, but A-Shell/AMOS does not). But under Windows, it is not possible to have two files with the same name in different cases, so I think we can be confident that there aren't actually multiple copies of the same file in the SYS: directory.
If the problem only affects the SYS: directory, then my guess is that your MIAME.INI file has an extra, overlapping definition of the SYS: directory, something like this:
DEVICE=DSK0:[1,4] c:\vm\miame\dsk0\001004\
DEVICE=DSK0 c:\vm\miame\dsk0\
In the above case, the first definition would define DSK0:[1,4] as pointing to c:\vm\miame\dsk0\001004\, while the second one would define DSK0:[xxx,yyy] as pointing to c:\vm\miame\dsk0\xxxyyy , resulting in two definitions for DSK0:[1,4].
If so, since DIR scans the DEVICE statements, it would probably display them twice (first one set of all the files, then repeating it).
If that isn't the solution, then let's have a closer look at:
1. The list of DEVICE statements in your MIAME.INI
2. A sample DIR SYS:I*/W output
3. A sample DIR DSK0:[1,4]I*/W output
(if 2 and 3 are different, that suggests that there is something funny in the ersatz table.)
4. A-Shell Version (from VER.LIT)
