Hey guys, can you do me a favor and check your order of things in the QMC\System\Setup\QDS resource\General tab settings and see if the order you have the Source Doc Folders there is matching what you see in QMC\Documents\Source Documents? If those match, that will explain why. If you want them in a different order, I will have to have a look to see how we can safely change things without breaking anything in your setups. In looking at things though, it appears you have a higher level folder with subtrees under that, but my hunch is things are showing in perhaps date modified order or something along those lines? I have not really dug into this previously, as I never really noticed until you pointed it out. If I can find some time, I will see if I can do a little experimenting here and see what I may be able to sort out, but I wanted to try to point you in a direction too, so you could see if any of the above make any sense or not.
It's actually defined by the file system and not by us, Windows states the following (emphasis mine) (http://msdn.microsoft.com/en-us/library/windows/desktop/aa364428(v=vs.85).aspx):
The order in which this function returns the file names is dependent on the file system type. With the NTFS file system and CDFS file systems, the names are usually returned in alphabetical order. With FAT file systems, the names are usually returned in the order the files were written to the disk, which may or may not be in alphabetical order. However, as stated previously, these behaviors are not guaranteed.
I hope this helps for now. I will push for improving this in future releases.