[TYPO3-english] Duplicate entries and missing files in 6.2 Filelist

[Scotty C]

Hi everyone,

I've just completed my first upgrade to 6.2.6 LTS from 4.5LTS. Everything works except one strange occurrence with my files. In my PuTTY shell I can see my file listing:
-rw-r--r-- 1 user user 8753 Oct 24 00:26 styles.css
-rw-r--r-- 1 user user 1719 Oct 23 23:42 template.html
drwxr-xr-x 2 user user 4096 Oct 23 21:45 images/

Inside images/ I have:

-rw-r--r-- 1 user user 651242 Oct 23 21:45 background.png
-rw-r--r-- 1 user user 195100 Oct 23 21:45 banner2.png
-rw-r--r-- 1 user user 323131 Oct 23 21:45 banner.png

... However, in the Filelist, I see 
- styles.css *twice* 
- template.html is not visible
- images/ is present but when I enter the directory it appears as empty. Note: I do not mean "empty directory"; I mean, "empty column", "nothing".

At first I thought this was a permissions error, but then the images/ directory gave a blank page/column, so that made me reach out to you all.

As always, any input is greatly appreciated - thanks!
-Scott.