You are gravely mistaken. Agassi only has 209 Masters series wins. He's actually 3rd, behind Nadal who just surpassed him. Federer passed Agassi several years ago, (and was remarked on then).
If you have a source for this, I'd love to see it.
1. Roger Federer 252
2. Rafael Nadal 215
3. Andre Agassi 209
I think I might have figured out why the discrepancy.
If you go to this page for Agassi's records, it doesn't say "251" anywhere, but I added up all the wins in the ATP Masters Series table, and they add up to 251.
there's a note on the page underneath that table: Tournaments were designated as the 'Masters Series' only after the ATP took over the running of the men's tour in 1990.
So, Andre's wins at some of these tournaments from 1987-1989 (Indian Wells, Miami, Rome, Canada, Madrid) before they were designated "Masters Series" don't count as wins at Masters Series tournaments. I guess.