I was able to help my Dad solve this problem by using SysInternals perfmon to see what the process was doing. Thanks to the earlier posts about the initial startup calling out to github I could see the process was constantly searching the system PATH for git itself. It somehow copes without having git installed on the machine but progresses very slowly. By starting again, clearing out the folders mentioned but this time installing git before hand, it completes the update very quickly (less than 1-2 mins) and the program starts up.
N.B this was on Windows, I'm guessing it may not impact other OSs that normally come installed with git i.e OSX or perhaps it's just a case that people are using git for other projects so there's no impact.
Whilst I'm here, is this app itself hosted on github? Would happily try and add a progress bar or at least some logging.
Richard