I do not see any problems with your config file after resuming from sleep on Windows 7 (32 bit). Here are screenshots before going to sleep and after awakening the system. As you can see, clocks keep their respective positions.
Clocks positions are stored in user configuration file
. You may be interested in recording what you have there before the problem occurs and after you see it.
I think something else may be interfering here such as a virus, or other malware that may be messing around with World Clock ini files, and perhaps with the binaries as well. I don't see any other logical explanation to the described behavior.
Please check your system and make sure it is malware free.