When you launch your browser it loads your start page before it loads extensions. Then all the extensions you've installed start gathering the information they need to work. In AdBlock's case, it's fetching the filters from the filter lists you're subscribed to. Those lists contain a LOT of rules, and it takes a small but noticeable amount of time to fetch them all. If your start page finishes loading before AdBlock can pull in all the rules, unblocked ads can appear on that page. When you refresh the page, the ads are gone because AdBlock has had time to fetch and process the filters.
To get around this, set your start page to the New Tab page, or instruct your browser to launch with the New Tab page open first, followed by the pages you want to open automatically. Or, just reload the page. :)