Forget about WPtocuh Pro - this is just basic WordPres coding practice. You must not use hardcoded URLs - they must always be dynamic. It is very common for people to install their WordPress in a subdirectory, even for basic sites.
Also, my solution would be very simple to implement, as I could do it myself, but the problem with that is that every time I update the plug-in, I would have to re-apply my hack - a fix that you should apply yourself.
Is there anybody else I can talk to about this who knows anything at all about WordPress coding? This really is a very simple fix - once again, I can tell you how to do it.