It is illegal to retain an employee's passport and to refuse payments stipulated in law as a bargaining chip.
Your case is not unique. This is a common practice thus perpetuates such corrupt practices usually stemming from HR departments for as long as such practices are criminalized they will continue unabated.
The UAE is a signatory to the UAE Convention on Forced Labour which contains the provision which states withholding of passports is illegal. It is illegal anyway since it is your document (though directly owned by the Philippine government).
Further it is illegal under UAE Law by a decree issued in 2002.
While the UAE received bad press at time for human rights abuses in employment, these practices are imported from abroad. The real fault lies in a lack of criminal laws to combat this.
Also contact the Labour Department on its hotline 800 665I but I understand you may be referred to immigration or passed around which I suppose is expected.
If the Philippine Consulate is dragging its feet, you may consider contacting a lawyer for advice and filing criminal charges. Check out its fees and what you get back once you win. A case of this sort in the courts should not take long.
There are several articles on this relating to the government decree in 2002. Further your passport is the property of the Philippine government.