Is it normal that re-running the same tool still always brings new 'finds'?
1) Are you running it from the same network each time?
2) Are you actually selecting 1000 records, right-clicking, and selecting "Find Available PDFs", or are you trying in smaller batches?
Recall that, when you use "Add Item by Identifier" or "Find Available PDF", Zotero will actually load the DOI/URL page before checking for OA sources. The latter can change over time as Unpaywall updates its data and we incorporate it (which happens no more than once a week),
but the former can change based on whether you have access to a PDF from your current network and whether a site is blocking you.
We should probably put in some automatic per-site rate-limiting to keep those requests under control no matter how many items you select.
What would be even better, would be something like what 'Publish or perish' does for Google Scholar (quite effectively).
I've noticed that it sometimes can't retrieve PDF despite a correct link attached to an item.