If you installed the zip package first before doing the .apk, you had an edited .xml file. This file was read by the secure element and the signature on the hacked .apk in that zip did not match so it locked it out from using the chip. Its seems to be once the chip is locked out it cannot be unlocked (unless Google implements this in future GW versions).
This is why I got a new phone. The chip is separete from the OS and rom. No matter what you do you cannot fix the not responding issue unless an app was allowed to reconfigure that chip, which google wallet is the only one allows to access it, but it apparently has no way of "unlocking" the chip.
If you just installed the .apk on a stock experience, the chip recongizes the valid apk signature and key and lets you access the Secure Element. Its my understanding that if you install any other rom, do a factory reset, or whatever, that if you only install the "official" GW app (the one signed by Google), then nothing should go wrong with your phone. You may have the issue of your money not coming up when reinstalling the app, but a simple phone call to either money network or google (?) seems to fix the issue.
Although this is my theory, I have yet to try and install a new rom and see if this works. It sounds like this is the way the Secure Element works. It locks itself if at any point it does not see a valid Google signed apk. Since Google is the only one with the knownledge and access to this chip on a code level, I assume they have implemented within the chip their algorithm for apk signaturing. Any app that trys to access this element, which at this point, is just a hacked older version of google wallet, is not going to have the right Google signature, thsu the chip "shuts down" and new hardware is the only way to get it to return.