I have tried two different ways to add the old pushpin set in S&T2009. One way is to add the pushpin set using the microsoft proposed method. If i remember correctly, this is only adding new custom pushpins similar as the previous S&T2007 version, but they are not in the default pushpin region (probably this caused problem when using an old S&T file that expect the old complete pushpin set).
But another user in this forum has reported another method that i think may solve this problem. He has made an .exe tool that patch S&T2009. I have tried this other method myself and this replaced the actual 2009 complete pushpin set with the previous 2007 pushpin set in one single operation, so in other terms, it turns back exactly like it was in the good old days. I am guessing that if you import your old map file with 2009 modified with old pin set in this situation, it will see old pushpins in your map correctly because with my eyes, it looks exactly like it was before. But when using microsoft method, if i remember correctly, you have to add the pushpins one at a time and they are not in the default pushpin icon zone, but they are simply added similar as if you are adding some customs pushpins yourself.
i didn't try myself to see if this correct the problem, but give it a try, it may help a lot...
Here is the tool download area, so you don't have to search for it. Close S&T, run this tool and then open S&T2009 and you will see that the default pushpin set is like the goold old days (S&T2006 and 2007 version)