Hi Dhobs
I suspect the incomplete problem is related to a file permissions issue we normally see with either win 7 or vista operating systems, I believe its a regular occurrence if you didn't start WinMX as an administrator so could you try the following please :
Right click on winmx.exe and select "run as administrator" this should hopefully to fix the problem, the other way of dealing with this issue is likely the more common and that's simply to create a new folder in your root drive for incoming files (maybe called "incoming files") and the problem should go away.
I,m not sure whats going on with your other issue as its not clear exactly whats missing , the files themselves or the file types , or the treeview items missing ?