Since when this option enabled "git svn rebase" stays stalled and does nothing, I'm starting to think that it's not totally innocent. However since it's checked on the default setup, I would like to know what this option does, and why it should be enabled (I guess that it should be since it's the default).
Q: What does the "Inject ConEmuHK" does precisely ?
As is... what ConEmuHk is doing described in ConEmu docs.
In brief - it fixes many Win console problems and implements "inprocess" features like ANSI and "-new_console".
Internally - it hooks dozens of WinApi functions.
In theory, it must not break any behavior of running applications, but if it so - you need to report the problem on project issue tracker.
PS. Do you using last ConEmu build?