i read you guys comments but let me add another dimension. im involved with companies that have similar issues. when companies start, they have to then undergo a whole bunch of registrations. and while it sounds simple enough. it takes a couple months to get the company registration docs finalized, only then can you start the process with sars. dealing with sars is a nightmare. can take weeks but also can take about 6 months. not to mention the time it will take the accountant to prep and do the registration. if the accountant is really slack thats another half year with the registration sitting on his desk.
the guys advising you to ask for an IRP5... this may not help if the employer doesn't have his sars paye registration yet.
your employer may have misunderstood your requests for a refund. you aren't allowed any refund from your employer. all moneys deducted from you will still have to be paid over to sars. even if the registration is 2 years since they started deducting, it will be back dated and the funds paid over. your employer is offering you a different position. one which i have come across many a people that have taken up. being a "consultant" has its upsides and its downside as well.
my suggestion to you is. ask your employer what is the progress with the sars registration. if they want to know why you are asking, state that your 2013 tax return is overdue, and your salary and taxes aren't reflecting. (act intelligent) and state that you realize that if they not yet sars registered, they cant issue an irp5. and with out an IRP5, you cant submit your personal tax. your accountant has advised that failure to submit tax returns, sars issues penalties of R250pm. so you are get getting nervous as you don't want to start incurring the penalties.
state that, gauge their response and take it from there.