The first thing you need to do is apply for a stamp3 at GNIB. You also get a GNIB card along with the stamp3. Tell the guy at the counter that you are a spouse of an E.U citizen and you are eligible for a 1 year stamp3. For details on various stamps see here...
http://www.mrci.ie/know_rights/legalsta ... idency.htm
GNIB also requires that you bring a letter from your spouse's employer stating salary amount, and how long he's been working for the company, and proof of health insurance, so make sure you take that as well.
IT's basically a game of chance, if the guy is a jerk/ignorant, try to go another day and hopefully you can see someone else who knows that you are eligible for one.
Reapply for the spouse work permit, then include copies of your GNIB card, stamp3,letter from your spouse's company giving his salary and period of employment,copy of spouse's passport, certified copies (by a solicitor) of your qualifications,letter from your firm stating that they are sponsoring you, maybe even a letter from your local T.D supporting your application.
Try to get your firm's solicitor submit the application on your behalf.The government doesnt seem to bother with applications unless a solicitor or a T.D is involved...seems like that's the Irish way of doing things.