I have same problem and I solved in this way:
disable atitool from autoloading at windows startup
disable to load any custom profile when atitool starts
reboot and start atitool
lock the divisor to any value is displayed, in my case is 4 with catalyst 4.12 and Radeon 9800
set new overclock or underclock profiles with the multiplier locked
Now ibernate and standby work perfectly!
If the coder of atitool is reading, please add an option to load automatically a custom profile after the resuming from standby as now (atitool 0.0.23 b10) after resuming, the default bios clock values are loaded.