Hi spencerokada.
The Pole has influence on the set up, as long we are talking about the 2D set up. This builds a disc like shape as orientation to the joints. With its initial position, this can change the set up. Adjust eh pole and it should be fine.
I have recorded a little clip for you, showcasing two ways to handle it. Adjusting the Pole, or set all you need and set the binding pose again.
Clip:
https://www.amazon.com/clouddrive/share/eCUHyQmVqKDPQzvcxPUDCOepOvISQd6i5WeziGajibq
As you can see the specific joint position here cause a flip while setting up the Pole, but it flips back in the moment I pull the Pole.
Have a look here:
https://help.maxon.net/us/#TCAIK-ID_TAGPROPERTIES
If you have a scene file, I’m happy to look into it, which is always the better way to handle things, a scene file is more often than not a clear information. As usual, please reduced to the problem, no extra stuff in it, like render tags or 3rd party lights. Thanks.
I hope this shares all the specific informations needed for now: (If you want to grow hugely in character animation, Bret is the way to go!)
https://www.cineversity.com/vidplaytut/create_ik_chains_quickly_with_c4ds_character_menu_commands
https://www.cineversity.com/vidplaylist/c4d_character_rigging_basics/align_copy_mirror_ik_changs_quickly_with_c4d_character_menu_commands
Perhaps more for the details—after minute 33.
https://www.cineversity.com/vidplaytut/siggraph_2015_rewind_bret_bays_weighting_workflows_for_cinema_4d_character
All the best