At least for me the SQL trigger doesn't work 100% of the time - even Shinto said it probably wouldn't be 100% effective. A few times I've opened my Yahoo account with 1 new email indicated and found 2!

I only use single message mode as well and the manual refresh isn't immune from the problem. Shinto mentioned a possible issue with the SQL fix and a write-ahead log DB so maybe that's getting in the way