I see the same under Windows XP with Architect 2.2.0.
The same happens in several other windows, like trying to drag and drop a component from root to some branch.
There is the popup for Move, Copy, and Link. It is not possible to press on anything else but Move.
We have a solution for this and it will be in the next patch. The issue is that some users don't have DirectX 9 installed and our growl notification uses css animations. Sencha Desktop packager and Chrome both hardware accelerate these animations using DX on Windows and when it's not there they don't show (see screenshot for what should happen when you save). Newer versions of Windows install an appropriate version of DX by default.
Typically the animation occurs and on animation end we clean up the growl message and so under normal conditions the pane that holds them is a 0px by 0px div and does not get in the way.
2. Make Architect viewport have more width so dialogs don't overlap with this pane and get "covered up"
We know there has been some regressions with 2.2 and mainly that's due to the new platform we're using. After we address the issues reported by the community things should smooth out. Thanks for working through this with us.
Also note that Architect 2.1 and 2.2 can be installed side by side simply by changing the install location in the installer to something different for the 2nd install (don't overwrite)
Sencha Architect Development Team