i know this is kinda vague, but hopefully someone can help me. i have a SQL Server that has 32 cores (64 logical). and for some reason, when we have a job that kicks off that uses 39 of those 64 CPU's and basically tacks them out. when that happens the SQL Service chokes for about 5 minutes until it's done doing what it needs to do.
That when you have a job that takes up a large number of CPU's, things slow down seems to be a natural cause/effect. One thing you might consider is reducing the parallelism by setting MAXDOP to a lower number. Sometimes when you have too high a degree of parallelism, it can work to your disadvantage. http://msdn.microsoft.com/en-us/library/ms181007(v=sql.105).aspx