Yes, there's a difference. Track frames usually have a slightly higher bottom bracket, so the seat tube measurement will be equivalent to a slightly larger bike. combined with a slightly different preferred body positioning on track bike (versus road), this usually leads to the suggestion that somebody ride a track bike that's 1 cm smaller than ideal road size. Of course, there's lots of variation based on body proportions (long legs, long arms...) and preference...
What should you do? You should test ride a 52cm and see if you like it.