I was able to reproduce the issue. The important steps you need to do are:
(1) Disable the RtcSync Tool in the registry
Rtcsync.exe will configure pins 194/196 as i2c, in order to access the external RTC.
According to your screenshot you already did this.
(2) Put all GPIO configurations into one single string:
set gpio.bootconf ="[colibripin_196] altfn=3 [colibripin_194] altfn=3"
While testing I noticed that the configuration string was stored only partially. We will need some time to investigate the reason for the failure. I will get back to you as soon as I have more details.