They are only hints that Tweak has altered the startup of the computer which is exactly what it is supposed to do. You now have some different items appearing on your Desktop like a different Recycle Bin and the main background which are most likely being loaded by default because they are faster to either Run, Load or both. Remember that Tweak is all about getting things started faster not necessarily keeping them the same. XP by its very nature is a heavy load on any computer it has high system resource requirements and enormous Overheads to run normally with just all of Windows Installed you'll have something like 40 processes running and it only gets worse the more software that you add.
Well I've just had a look on MS Web Page and when you type in Tweak Ui 2.1 you got a Windows 98 page for help which is useless to you about the only thing i can suggest is that you do as MS tell you on the starting Page of the Power Toys for XP as there is no documentation for the XP version of Tweak:-
Important
? If you installed PowerToys prior to April 23, 2002, you must uninstall your old PowerToys before installing the versions available here.
Uninstall it and hope for the best. while it most likely will not return the system to normal it will remove some of the potential problems from the system. I guess it's a "Suck It and See" approach as MS offers absolutely no help at all but if you want to look up the 98 listing for Tweak which they claim "We lost two week's sleep with this little lot... Desktop Are your desktop settings unchanged since the day your"
http://search.microsoft.com/search/results.aspx?view=en-au&st=b&na=82&qu=Tweak+UI+2.0
While it does apply to 98 maybe there is something in there which may be of some help to your current predicament.
Col