To be quite frank, if a school's adcom is so horrendously dense so as to dismiss you on the basis of "I've never heard of that" then maybe that school shouldn't be on your list.
IMO, where you worked or who you worked for prior to the b-School app should have minimal impact on your "chances" unless said conditions were actually very HIGH profile. Like, if you you worked at Enron you might have some explaining to do. If you came from Google then you might be regarded in a better light.
Anything in between shouldn't matter so long as you can demonstrate your personal value.
You said you had a good growth story etc. along with working in this small startup so lean on that! The Adcom should not be interested in anything (apart from hard grades) but how you as a person are going to benefit from their program (and vice versa, of course).
I think it's very important for your app AND for your future business career to understand that the reputation/value of a company does not necessarily equal the reputation/value of its employees, from the interns right up to the C-suite. Worthy schools and their adcoms already understand this.
I'm a current Corporate Residency MBA student at Dalhousie University (Nova Scotia, Canada).
This account is to help spread the word about this unique program, as well as to help provide a student perspective for MBA applications and GMAT experiences.
Every week I publish a blog about life in the CRMBA by interviewing current students. Find us on Twitter and Facebook, or post any questions/comments/concerns in this thread here on gmatclub.com
Highlights of the program include:
Specifically designed by Corporations/Employers, No work experience necessary, 8-month paid corporate residency, Grades/GMAT score not the main focus for admittance