I've been successfully running CCleaner (with a custom INI file) on Server 2003 for several versions. After installing version 2.28, I noticed that the "Analyze" process would not get beyond 70%. I also confirmed that CCleaner 2.28 is actually deleting the SYSVOL and a Temp folder in Symantec's folder hierarchy during the "Analyze" stage. Version 2.28 appears to be working fine on my Windows 7 machines (also with a custom INI file). Here are the contents of the INI file I use on Server 2003:
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Language=1033
UpdateKey=01/17/2009 10:29:52 AM
DelayTemp=0
MSG_CONFIRMCLEAN=False
BackupDir=C:\Program Files\CCleaner\Backups
WINDOW_MAX=1
WINDOW_LEFT=0
WINDOW_TOP=0
WINDOW_WIDTH=620
WINDOW_HEIGHT=450
BackupPrompt=0
(App)Autocomplete Form History=True
(App)Custom Folders=True
(App)Desktop Shortcuts=True
(App)Installer=False
(App)Start Menu Shortcuts=True
(App)Windows Log Files=False
Include1=PATH|C:\|CG Cache
Include2=PATH|D:\|CG Cache
Include3=PATH|E:\|CG Cache
Include4=PATH|C:\|MSDownld.tmp
Include5=PATH|D:\|MSDownld.tmp
Include6=PATH|E:\|MSDownld.tmp
Include7=PATH|C:\|Temp
Include8=PATH|D:\|Temp
Include9=PATH|E:\Temporary Internet Files\|*.*
Include10=PATH|C:\|WUTemp
Include11=PATH|D:\|WUTemp
Include12=PATH|C:\Documents and Settings\Administrator\Cookies\|*.*
Include13=PATH|C:\Documents and Settings\Administrator\Local Settings\History\|*.*
Include14=PATH|C:\Documents and Settings\Administrator\Local Settings\Temp\|*.*
Include15=PATH|C:\Documents and Settings\Administrator\|UserData
Include16=PATH|C:\Program Files\|WindowsUpdate
Include17=PATH|C:\Windows\|.j*
Include18=PATH|C:\Windows\|CG Cache
Include19=PATH|C:\Windows\|MSDownld.tmp
Include20=PATH|C:\Windows\Temp\|*.*
Include21=PATH|E:\Temp\|*.*
Include22=PATH|E:\|WUTemp
Exclude1=PATH|C:\Documents and Settings\Administrator\Local Settings\Temp\|1
Exclude2=FILE|E:\Temporary Internet Files\|desktop.ini
Exclude3=FILE|E:\Temporary Internet Files\Content.IE5\|desktop.ini