I would suggest increasinge thread usage, this is documented here. My general guideline is the number of physical processors x100, 1 processor 100 threads, 4 processors 400 threads.
If those steps do not fix the problem, then a deeper dive into the performance needs to be considered. If you are using 2006, there are some performance counters that come installed. What I like to look at is the BizTalk:Message Agent, there I like to look at Message publishing throttling state. How do we get to there?
Bring up Performance from Adminstaive tools or c:\perfmon from a dos prompt click on System Monitor and the + sign
Let me not forget the link to Microsoft’s official performance information here, and please refer to the disclaimer on the side of my blog.
This should get you well on your way to finding out what is going on, and being able to improve performance of your BizTalk setup.