You haven't really given us much information to work with, so I'll guess:

In broad terms, SQL Server stores a query plan for the whole stored procedure. That plan will be tuned according to the values passed to the procedure as parameters the first time it is executed. If those particular parameter values are not typical, the server might store a plan which doesn't work as well when executed with different parameters. Google 'SQL Server parameter sniffing' more more information.

Alternatively, post some more details to get better answers.