I believe that they're very strict about this. An acquaintance of mine got his visa and entered Brazil within the 90 days, but received an almost illegible entry stamp. The next time he tried to enter the country, the immigration agent said that he had not entered within the required 90 days and was going to deny him entry. After thumbing through his passport several times he finally found the entry stamp from the previous trip (apparently it was almost illegible and overlapped a stamp from another country) and convinced the agent that his visa was in fact valid.