Martin Karing thanks for the additional details. Were there any other changes in your environment which might be involved?
Have you bisected the plugin changes between the working and the non-working state to identify the specific commit, or is your suggestion of PR544 an educated guess? I don't see anything in PR544 which should alter the authentication used by the plugin. Stephen Connolly may have a better assessment than I do of possible credential related side effects in that pull request
If you haven't bisiected the changes, would you be willing to do that? If you're not comfortable compiling the plugin for each of the commits, I can provide compiled versions of the plugin for you to use. I can't duplicate the problem, and am not willing to install and configure Bonobo Git Server, since I don't have a Windows Server license and my Windows client machines don't have IIS installed.
Also, you flagged in your comments that you're using http protocoi, yet the log shows https protocol. Can you clarify if you're using http or https protocol to access the repo?