Todd, let me make sure that I understand your senario before I post an answer.  Am I right in saying that you have Parent table A which can or does have multiple Child table B records. Each Parent table A record requires that a single file be created to contain...

1. A single Parent table A record and...
2. Multiple Child table B records for the Parent A record.

Are you saying there are around 3 million of these parent records?

I think that the slowdown in your file creation rate "sounds" like mem-to-leave or other memory pressure.

Can you correct or confirm my summation of the issue before we go on?

Thanks,

Zach