I think I may have found the problem. Need another IsBoxer update to test.

So setting all clients to use all CPU's instead of an 'per' core basis did not work.
Setting the startup time from '1' to 5, 10, 15 seconds did not work.

However, I think the problem is when IsBoxer updates itself it re-installs a shortcut on my desktop. When that shortcut is re-created, the shortcut itself loses the Admin settings.

As soon as I changed the shortcut to 'run as administrator', like it was when I first installed IsBoxer all my client switching worked like a charm. Multiple client startups.

I believe this is what the problem was (windows 7, 64). I'll double check the next time I get an IsBoxer update to see if it is in fact removing Admin privileges. As a quick test though, I did remove admin privileges and sure enough my window swapping sequence did not work anymore.