Not sure why this is happening, but try this. This is the way I've done it. First, make an alias of the folder (File>make alias) and put it somwhere, like Documents. Then, copy drag it (Option-click) to the part of the dock below or to the side of the separator near the Trash icon. This will place an alias of the folder in the Dock. You must keep the first alias you made.
You can also make one just for Utilities, the same way. The app folder will appear with an A and the Utilties folder will appear with an X.
EDIT: It's been a while now, but I think I got rid of the default app folder because I didn't like the way it looked and functioned.
You can also see I put an alias of my home folder there, as well.
Might as well mention another customisation. Get Tinkertool (free) Go to Dock>Disable Dock Expose to get rid of the very annoying -- at least to me -- entire screen turning black when opening one of the Dock icon's options.
http://www.bresink.com/osx/0TinkerTool/download.php5
Message was edited by: WZZZ