Is this the same issue as described in this thread?
viewtopic.php?f=4&t=91720
One thing that might be useful in troubleshooting is that in the ATEM 8.0+ firmware, there is now a small timecode section in the ATEM software control panel. So you can use this to monitor the timecode being generated by the ATEM, and can also use it to set the initial timecode being used by the ATEM's internal timecode generator (if not feeding in external LTC).
So you might be able to use this to help determine whether the ATEM is correctly reading the external LTC timecode at all in 50p mode. And also whether the ATEM is able to embed timecode that works via its internal timecode generator (rather than an external TC source).