S3 I can't help you with but try this for Hibernate.
If you don't want it, please test it for me once and let me know if it works.
Create a new shortcut (right click empty space, click new, click shortcut)
Put this on the target line
C:\Windows\System32\rundll32.exe powrprof.dll,SetSuspendState
And name it Hibernate. You can pin it to the top of the start menu for example. This should allow you to at least enter S4 sleep - I still can't get S3 to work on the system that has sleep problems - with or without Chameleon booting it!
EDIT
I have since fixed my own Windows sleep issues by making the Windows HDD the default boot HD and not using Chameleon to boot Windows. S3, S4 and hybrid sleep now works perfectly. Apparently Windows 7 refuses to hibernate if it's not on the first drive/boot drive in the BIOS.