I have noticed this too, but have rather idly not done anything about it until now. I am currently using 2221 on a Vista machine, and 2175 on a Windows 7 machine. Both exhibit this behaviour, but version 6.0.7 on my XP machine does not.
Context menus for drives also show this behaviour, but with different entries for the two icons, which make it clear that one icon relates to the shortcut file and one to the drive itself. I assume that the same applies to file/folder shortcuts, but in that case it is virtually impossible for the user to distinguish between the two icons, as both have the same context menu entries. I'd guess that the upper icon relates to the shortcut file, and the lower one to the file/folder to which it points, but it is clearly unsafe to rely on that. It is almost certainly wise in these circumstances not to use context menu erasing with file/folder shortcuts on the builds that show more than one icon on the context menu.
Unfortunately, these issues do indicate that some further thought is needed on the whole context menu issue. It seems odd, to say the lease, to add a 'Secure move' option for drives for instance. I'm happy to post a ticket in Trac, but I'd like to know what Joel thinks about all this before I do so.
David