ask to see if you can sign a NDA specifically with respect to the stock agreement, maybe?
i'd also find out from your lawyer, if you can, exactly what your rights are. have you been officially working for them? is that code technically still yours? what other things have you signed? etc..
just because they have and are using your code might not necessarily mean that they can continue to do so without your permission, if you didn't sign anything.
/not a lawyer
Also if you think they are not honest trust me it is not worth trying more, down the road they'll try something else to get back the stocks even if they give it to you now.
If they are not honest with you take your code without telling them and start you own company or if you need a job find other one. It is very difficult to get the dishonest people straight, best thing is to find your way out.