I've worked with this before. At a previous startup I was the only startup member that had deployed a significant web application. I had always used the FreeBSD platform. We deployed on Windows Server 2003 because despite my personal experience and the ability to pay for FreeBSD support the powers that be were nervous. At the end of the day 'you don't get fired for buying Microsoft' won the day.

As you can see, this wasn't a healthy startup environment to be in where fear wins over experience.