Because the apps are being essentially stored as XVDs, kinder similar to virtual discs I guess? Windows isn't playing nice, and seems to generate a whole host of potential problems, I kept seeing 'disk has been surprised removed' errors in my event viewer and I got curious and looked into it, then I found this guys blog who explains it in more detail.
Tweaker does indeed fix the problem but its more of a bandaid fix than anything, I've noticed very little problems using the steam client. This could also explain why people had a lot of issues earlier in the year, and some 'lost' disk space when they didn't uninstall properly.