Hi Adam,
No luck so far, so we've decided to use ART to simply drop and regress out the initial scans. Not the most ideal solution, but it seems like the only way preprocessing for the functional images will run successfully.
To drop the initial scans with ART, when the popup comes up to define ART thresholds, check off the box in the bottom left corner that says "Drop initial scans" and it will allow you to specify how many scans you want to leave out.

I've also started running into issues with the Structural Segmentation and Normalization. Just wondering - have you been running into any similar issues?

Hope this was helpful, and hopefully there will be a better solution to resolve this issue soon!
Best,
Melissa