We're still working out what the exact cause is. We've narrowed it down to 2 lines of code. Both of these lines of code are in a 3rd party zip library we use to bundle up the updates. This code hasn't changed in 2.6.16 vs. 2.6.16.3. It's exactly the same. So downgrading won't help.
We also believe this problem was in 2.5.x and 2.6.x, however it didn't rear its ugly head. Or if it did appear in the wild no one reported it.
We also noticed that sometimes building the updates works, sometimes it freezes on one of the files. So from now until we find & fix the actual cause of the problem the best solution (of several bad solutions) is to try building your updates multiple times. That is, if it freezes on a file, close wyBuild reopen it and retry building your updates.
Also, it's odd that this problem is only effecting your files. None of our test cases are effected at all (no matter how many times we run them).
In short: this is a very strange bug.