Update:
Turns out that Cutadapt is working fine in a workflow now. Based on that result, reconnecting the workflow “noodles” will likely solve your entire issue as well. Make sure you are incorporating the most current tool version (all steps/tools) to avoid older-but-fixed problems.
Test history and workflow if you want to compare your work to our test. I’ll leave this shared for a while, may help others, too.