There are so many things wired up to that pi, with no clear overview of what goes where, that it would be difficult to spot all relevant parameters to take into account in my response.
... keeping it brief then, I haven't personally seen any report of failing USB ports on the zero, though I'm sure there have been some. If you didn't test the bare Pi before embarking on the hacking job though, only you can troubleshoot this one most likely.
Alternatively take additional shots that gives the full picture of what you are trying to do, and any software modification you would have performed, who knows one of us may be able to spot the culprit...
