I have received a few mails regarding this particular problem in Windows Vista. The taskbar doesn't have transparency even Windows borders are transparent. One of those mails is as following:
I have a problem that I don't think anyone has come across or posted yet: My Vista task bar refuses to turn transparent. I enabled transparency to use Aero but while my window borders turn transparent my task bar doesn't; and it will not change color when I change that using aero, too.
Actually this problem occurs while using 3rd party software toolbars in taskbar. So if you are also facing this problem, then make sure you have not enabled any 3rd party toolbar in Taskbar.

The person who sent the above mentioned mail was using "iTunes" toolbar in taskbar and his problem was fixed after removing the toolbar by right-click on taskbar and uncheck the toolbar from "Toolbars" menu.

Many times a few branded PCs also come with their manufacturer toolbar enabled in taskbar which causes this problem.
So when you face this problem in future, make sure to disable any 3rd party toolbar in taskbar.
This article was posted by VG in following section: Troubleshooting, Windows Vista.
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jjthehey
Hey VG,
I have the same problem, but i don't have any toolbars in the taskbar and it is still not transparency. I uninstall the last program i installed cause i think it had a virus or something. Well if you can come up with a idea?
VG
^^ Are you using default Aero theme ro any 3rd party theme?
Jeet Chowdhury
like powerdvd 7 does. i noticed it about 6 month ago. and then i thought maybe modify registry can enable tranp... while 3rd party toolbar also on. i failed. i turn off 3rd party toolbar.
btw i think ms need to hotfix it and also 3rd party company need to update there software.
Sunny
I don't get this problem, because I use Vishal's excellent AeroVG theme, and one of the features is the permanent transparency of the taskbar.
Jeet Chowdhury
^^^^^
Chad Varquez
i think this happens in W7 too... when i open the Adobe Audition, the taskbar and windows does'nt use the aero theme anymore! but when i exit the program, the aero theme is now again used! y does this happen?
VG
^^ Its not a problem. It happens when you run a program which is not compatible with Windows Aero theme. Windows switches to Basic theme automatically.
Chad Varquez
ok.... but i think there's still many bug in W7...
Josh
Thank You!!!! Worked perfectly.
levitation
That's it! It worked! The MediaMonkey toolbar was the culprit for me.