Paying salary less than what is mentioned in work permit

[tier1_to_ilr]

One of my ex-employers used to pay me less that the salary mentioned in the work permit. This was between sept 2006 and March 2008. It used to promise all employees a fixed salary that local employees would have got with gross salary mentioned in work permit. And it used to claim all the tax benefits that an offshore employee would have got. e.g. my gross mentioned on WP was around 31000. By that logic gross in monthly pay slip should be approx 2580. But it used to be around 2200. After March 2008 my gross started matching that of WP. In April 2009 we got an email from finance that we should sign a self assessment form with beneficiary name as employer's name. It also mentioned that you have to do this because you are promised only a fixed monthly salary. Probably by that HMRC would have changed the rules so that employer could not claim tax benefit without employee's consent.
Any opinions whether my ex-employer is legally correct?