I may have made progress concerning this issue. If you compare the settings of two C::B compilations - one using wxWidgets 2.6.2 and the other using wxWidgets 2.6.3-RC2 then C::B saves the settings differently as following:
This is how it's done with wxWidgets 2.6.2:
<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<CodeBlocksConfig version="1">
	<app>
		<main_frame>
			<layout>
				<view1>
					<DATA>
						<str>layout1|name=MainToolbar;bestw=308;besth=23|name=CompilerToolbar;pos=319;bestw=342;besth=23|name=DebuggerToolbar;pos=672;bestw=215;besth=23|</str>
					</DATA>
				</view1>
			</layout>
		</main_frame>
	</app>
</CodeBlocksConfig>
...and this how it's done with wxWidgets 2.6.3-RC2:
<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<CodeBlocksConfig version="1">
	<app>
		<main_frame>
			<layout>
				<view1>
					<DATA>
						<str>layout1|name=MainToolbar;bestw=792;besth=26|name=CompilerToolbar;pos=803;bestw=792;besth=26|name=DebuggerToolbar;pos=1606;bestw=792;besth=26</str>
					</DATA>
				</view1>
			</layout>
		</main_frame>
	</app>
</CodeBlocksConfig>
As you can see the issue is that 
bestw is computed differently (wrong in the case of wxWidgets 2.6.3-RC2). This results in the toolbar being too wide. Now we have to dig into the source code of C::B first to see where this is calculated and whether there maybe a bug inside C::B...
I don't have the time to do this now, but I'll have a look into it tomorrow.
With regards, Morten.