Mary, In Moodle pre 2.0 file icons were definitely present inside folders whether they were created in Moodle or uploaded as .zip files see attached screenshot of our 1.9.* site
This is a screenshot of the same files (yes they have had the names changes for clarity purposes) in Moodle 2.2 and yes they were uploaded as a .zip file into the course and then extracted as they were above, but this time using the Moodle 2.* method.
I thought it may be something to do with the renaming of the files and the missing Thumbs.db file, so I uploaded a different zipped folder of files and got the same result. Here's the really weird part though, in the 2.2 screenshot if I click on "Edit" and then on the cog icon next to the folder in the next screen then I get the screenshot below.
Files showing associated file icons!
It may be this is how it is supposed to be, but if so, why show the file icons at all if you just add them as single resources into a topic or week section in a course.
This really shouldn't bug me but the visual detection of a file extension is really important for many pupils especiallt SEN ones at that!