Now, I can't check this on my 4S (no jail break available, yet ... darn it!), but when I upgraded my iPad1 to iOS 5 and [re] jail broke it, I also discovered that some themes did not work. As in, some of the stock icons did not theme, while others did.
Turns out that Apple changed the name of many of the stock icons (well, at least on the iPad). From my reading, it appears that's the same case for the iPhone on iOS 5.
So, try this: SSH into your phone (or get into the Themes area on the iPhone using whatever method you use) and change the name of the Mail icon in your theme to Icon.png and
Icon@2x.png. The new bundle ID is com.apple.mobilemail.
For the Phone icon: Try icon~iphone.png and
icon@2x~iphone.png with the Bundle Id = com.apple.mobilephone
For the Music icon: Try icon.png and
icon@2x.png; Bundle Id = com.apple.mobileipod
And, the Videos icon: It's icon.png and
icon@2x.png; Bundle id = com.apple.videos
When I changed the names on my iPad, the icons changed. So, that leads me to believe the themed icons are
in the theme; the names just have not been changed to Apple's new names. Changing every name for those icons that
didn't theme helped me get my iPad theme working, so maybe that's what you need for the iPhone...
Again, I can't test this - but try it and see if it works?
Marilyn
P.S. Sorry, but the forum makes the @ names e-mail address links. Still good names, just cut 'n' paste or use as is...