Hi, from my experience, the SD SanDisk in the past gave me always the troubles even when apparently was working well, they gave me the same troubles like your with Homebrew apps. Because these SD has the tendency to have corrupted clusters soon or later. Once I changed SanDisk to Samsung I never had these problems anymore.
Anyway, let's suppose for now that your it's working well, I try to guess because the info from your side it's not so many. Let's say that you run Haxchi, and you open the app by the Wii U Menu Channel. So, if you open it by the Wii U channel and use the Wii U controller and run Nintendont, from Nintendont app you cannot use any functionality to update the app by the internet or it will gives you the errors or freezing the app. Because, to emulate the Wii U PAD the vWii has the internet Wireless Channel busy to keep connected the PAD. So, to test to upgrade anything, try to launch the app from the vWii and see there what happen. If you still has the problems, and if you have installed everything correctly, from the CFW a to the app and so on; the unique problem that comes in my mind, for absurd, it's the SD Sandisk.
Let me know....