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It depends on the program and whether you take any math classes in addition to the normal masters coursework. Certain schools are known for having rigorous MA programs that are excellent preparation for - and predictors of success in - PhD programs (eg. LSE) while others are not (pretty much any US econ MA program). However, if you do end up going to a slightly less-rigorous program, you may be able to make up for the math deficiency by taking extra math classes.
If you want to know if having an MA from any random program will help with PhD applications, the answer is no. But an MA from certain programs will help, and so will taking the time while in an MA program to remedy deficiencies in your background.
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