Where are you booking? I myself have never used Agoda but have used other OTA (Online Travel Agency) for flights & hotels and haven't had any major problems. I mostly book direct with certain chains for premier benefits and pretty much everything else through hotels.com. Some OTAs have price-match policies so that might be something to look into.

Eta, reread and see Thailand. Is it a chain/well known hotel or something small with limited reviews online?