Hi and Welcome to SevenForums
As you say this will i thing be a difficult issue to solve
I would tend to blame the particular apps involved rather than the actual OS as the OS works with the vast majority of applications.
You could try reporting the problem to Google as Chrome is in Beta and the more feedback they get on any issues the more likely they are to be addressed. With the official release of Windows 7 imminent, it's not in Google's interest to have any problems with their browser
One thing to try is to change the app icon for another one to see if the issue is caused by a non standard icon size.