Which labor office was that, and what kind of employer is it (industry and type of business)?
The municipal labor department has no authority to handle tax or insurance, though at the very least they should have told you they can forward your communication to the local branch of the Bureau of Labor Insurance.
You can report the irregularities to the tax office (NTB) and the BLI, and they'll probably ask you for more information/evidence in Chinese rather than take the initiative to investigate.
What the labor department definitely can do is conduct mediation between you and your employer (expect it to take a few weeks to arrange), but that's usually the last step before going to court.
The labor inspection office (or whatever they're calling it these days -- it belongs to the labor department btw) can also investigate the employer for labor standards (overtime, safety, etc.). In Taipei they have a new office in Wanhua, apparently; I'm not sure if the one in Jingmei is still there.
Requests for inspection can be made anonymously (i.e. the inspector won't be allowed to reveal your identity), but they always say that limits their ability to take action and suggest you check the box giving them permission to say it's you.
My understanding is you need to show the tax evidence, not just a labor contract.
It's perfectly normal to call part of the wage (or salary, same thing) a food allowance, and the tax and labor authorities normally do recognize this as part of the wage, as long as it's accurately reported. (See Art. 2 of the Labor Standards Act.) If you don't get anywhere with requests for inspection, but you have proof that you're paid the allowance every month, talk to a lawyer.