Ah, once I looked at the source I think I know where the problem is!
This is the place where the first message is thrown:
It should not throw this message because HOME_IGNORE_LIMITS is YES in my config. However it does.
This is my config:
As you can see there is no line break at the last line - which is HOME_IGNORE_LIMITS = YES. So I think the missing line break is the problem. I'll try and be back in a minute.