Towelroot, or any other root method shouldn't have any effect on the actual operation of the device. What is happening is there are new seLinux security enhancements built in to kk. Apps can now only read/write to folders they create/own. If another app created the folder, or if it was created by the owning app before the new security was implemented, seLinux will not allow that app to use it. More and more people are having problems even after the platform.xml edit which makes me believe its got to be done before flashing, or a factory reset may be needed. Im not sure on that right now.
The platform.xml edit is only for the external sdcard btw. You have to disable seLinux to solve this on the internal one. (Looks like this may also be true for external now, but like I said, im not sure about that yet)
There's an app in the store, I think its called sdfix, or sdfixer or something similar (search seLinux mode changer) that people have had some success with, so try that first.
Alternatively, I can mod the stock kernel to disable seLinux there. (May do this today anyway).
It's perfectly fine if you're not comfortable flashing kernels, but its really nothing to be too worried over. A custom one like ktoonsez kt747, will flash and run normally, and you have the option to learn more if you like so you can configure it how you want.
If you have any specific concerns about it, feel free to ask us. But in the end its up to you if you still want to refrain from flashing one.
Another thing you can try is to rename the apps folders, then reinstall it and let it recreate them. Then copy the contents of the old into the new. Not totally sure it would work as I expect, but in theory it should.
Anyway, if nothing else, try that app I mentioned. And let us know how ut goes!