Sreekant,
I do not think you need to rescale temperatures after NVT. Do you reach a stable temperature after all NVT steps? If not, check your drag coefficient or perform longer simulations. I would suggest to test your NVT and NVE simulations without the restart file option and verify around what temperature your system fluctuates during NVE. But, I am sure it is not an issue of the restart option.
A simple way to test that everything is working OK before long simulations, is to perform NVE steps only at a given initial temperature (without any rescaling steps, only initial velocities). Your system (Silicon) should equilibrate around 0.5*Tinit.
Javier Goicochea