The other issue may be the airport you enter at. I was drawing scrutiny in Bangkok (DMK) but then had not problem in Chiang Mai (CNX). Bangkok is the worst for potential problems.
Can you buy a re-entry permit before you leave India? That's how it works here in Thailand... if you have a student visa and want to leave and return again. But if you leave without a re-entry permit, the student visa is automatically cancelled.