Here's what I used to fix this same problem. Don't hold your breath for eBay to fix it.
Go to My eBay dropdown on the top right of any page and select Saved Searches. Then for EACH active search, click on More Options on the right side of the page, and select Stop Email Alerts. Then wait for a few hours (I waited 8 hours, and I also signed out and back in to eBay during this time) and go back to the same place again and select Get Email Alerts for every search you want activated. This should fix the problem on the next round of emails (mine come in at 4:30 am).
This will also give you a chance to clean up some old searches you no longer want. Happy searching and buying!
