Poor performance after applying SP4

Hi there, yesterday we applied SP4 on our SqlServer 2000 server running Windows 2003 and instantly we
had problem with performance. Queries that used to run for a second or two now runs way past 4 minutes. Does anyone know what we could do to locate this problem? By the way, SP4 was applied due to the fact that BizTalk2006 needed that SP in order to work properly.

BR
/Anders