I remember reading a study (it is pretty generic and I'm sure done many times), where a research group put a stereotypical 'white name' on a resume and sent it out, then put a stereotypical 'black name' on the same resume and sent it out. I'm sure you see where this is going in that the 'white' resume received many more calls and interviews. This bias is unfortunate but pretty prevalent in most organizations, and is even seen in university admissions frequently (same ethnic bias, different reasons).

I have had several professors/GTAs at uni who are native Indians that I highly respect for their CS knowledge. The accent can be a little hard to pick up at first if you've never been around it but after that its all gravy :) Likewise I've had some who I've completely despised, just like every other person of every other ethnicity. I'm sorry you have to deal with that.

Edit: expand on last para