I'm wondering if you might be able to get around this using rules instead of defaults. For example, you could try adding a node to your main repeating data source (doesn't have to show on the form) called "Set" or something. When a new form is started, in the form load rules, or any time after your query for the correct secondary data is completed, set that new helper node to 1, or "go" or whatever. Use rules on the set field to set all the main data source nodes - you can use a count of preceding siblings to get the correct 2ds node. You might want to make a copy of your current form, and try switching over to this technique - and not worrying about getting the correct value for each row to start - so that you can quickly test and see if the approach succeeds in the browser w/out the rule count error.
Another thing to check might be rules on your fields that have default values -you may have some side effects there. You could simply disable any rules, see if the issue still occurs, then debug from there.