Two MScs? I wouldn't be worried about the ex-Poly label to be honest. As long as you submit a strong application and if invited, interview well, you stand as good a chance as any.
The one thing that would concern me (speaking as someone who did their PhD after two Masters - though I had a five year real world working gap) is the two similar MScs may give you a perceived perpetual student label. You will need to explain why this is not the case.
A good first degree will probably be as good a selling point as any here, to give you a variety of knowledge and skills to take into a potential PhD.
Best of luck.
Ian