The reason this behavior is not noticed in VS2008 is because Microsoft had made changes in VS2010, namely changing the build platform to MSBUILD. Based on how MSBUILD works and how we need to cycle through every user file for each project to modify the instrumentation state; the larger the project number, the longer it will take for us to turn on instrumentation. Unfortunately, this is working as designed and the only option is to request an Enhancement Change from Microsoft to change the build sequence. So long as you leave instrumentation on, you will only see this delay hit once until you turn it off again.
NOTE: Changes to the code logic in 10.5 have sped up up the turning on/off of Instrumentation