Hi Chris,
I just did a simple test by starting two instances and upload same attachment, but they are saved to repository with different names, one has (2) as suffix, the Name Conflicts setting is same as yours. Can you tell how many instances are showing the same entry ids? And for those instances, the attachments are saved indeed with (2), (3) after names, or not saved at all? The files list you see is stored in Forms database, you can use the query to get the history data for the STR step.
select * from dbo.worker_instance_history_extended_data wid
left join dbo.cf_bp_worker_instance_history wih on wid.history_id = wih.history_id
where wid.bp_instance_id in (280973, 281167) and wih.step_id = @STRSTEPID
update the STRSTEPID with it's real value, include more instance ids if you can find.
The history_context column stores the data that will display on the Monitor page.
What I want to figure out is whether somehow the history is mismatched that those instances retrieve same history out, or attachments are always imported as same entry id.
You can file a support ticket after getting the results, and provide us more details about your design, if you can still reproduce it, etc.