The VTune forum (Intel VTune Amplifier XE and VTune Performance Analyzer http://software.intel.com/en-us/forums/intel-vtune-performance-analyzer/ ) is a better place for help on VTune questions.
You'll get help there from VTune experts.
In general "tuning for startup" shouldn't be too different from normal tuning.
But startupmay be doing different work than your software normally does.
The challenge might be more trying to figure out why the system went idle during startup (locks, IO, network, system calls, etc).
Please try the VTune forum and see if they have suggestions.
There is possibility of AV interference with the normal startup.It is known that Kaspersky AV will hook or detour patch whole the process and thread and context switching API functions.So this can incure some perceivable lag.
I would advise to monitor your application startup with the Xperf tool.