For those who may run into this, the issue was that only the first 16 (IIRC) bytes of an agenda item was hashed. Since our agenda items were full paths, there was a lot of repetition in that first 16 bytes and a job would be run repeatedly.
The workaround was to add a counter to the front of the file paths, and I believe in the future PFX will be making it so the first 256 bytes are included in the hash.