Which icon isn't appearing?

The stop icon and it appears to be position dependent. Left of the reload it stays, but grayed out. Right of reload it gets combined with reload and only displays when it is active. Bookmarks icon is similar. If the menu bar is turned off it displays. Thanks

That is intended. You only see the Bookmarks Menu button if the menu bar is hidden.

Firefox 4 has two bookmark buttons with a star in the Customize window.
One star button has a drop marker that open a Bookmark menu.
The other star button without the drop marker opens the bookmarks in the sidebar.

You can drag the Bookmarks menu button with the drop marker in the Customize window from the toolbar palette on a toolbar (e.g. Navigation Toolbar or Tab Bar or to the left side of the Bookmarks Menu Items).
You only see the Bookmarks menu button if the menu bar is hidden.
If the bookmarks toolbar is visible then the default bookmarks menu button will appear on the right hand side of the Bookmarks Toolbar as part of the Bookmarks Toolbar Items.

Firefox 4 uses a combined Stop/Reload/Go button that is positioned at the right end side of the location bar.

To move the Stop and Reload buttons to their position to the left of the location bar you can use these steps:

• Open the Customize window via "View > Toolbars > Customize" or via "Firefox > Options > Toolbar Layout"
• Drag the Reload and Stop buttons to their previous position to the left of the location bar.

• Set the order to "Reload - Stop" to get a combined "Reload/Stop" button.
• Set the order to "Stop - Reload" or separate them otherwise to get two distinct buttons.

Thanks.