David-
What you are experiencing only occurs the first execution after a host restart, which on a production server should be infrequently. Like any other .NET application BizTalk assemblies are only compiled to MSIL. On first execution JIT compilation takes place so it takes a bit longer than usual to execute. I don’t know of any work around and it is in my understanding happening “as designed”.
For this reason I suggest that before doing any perf testing, (or before demoing BizTalk to others) that you run sample messsages all the way through the process, (JIT happens more granularly than the assembly level). This will get the JIT "out of the way" and be ready to rock!