preferential amplification by proofreading Taq ???

[DHolst6016]

It is strange that you have problems amplifying the same size product with
Taq and proofreading Taq.  One would suspect nonspecific priming.  One
thought my be that since Taq polymerase has such a broad activity range,
30-85C, nonspecific priming may be an answer.  Possible solutions may be
hot start PCR or use af a proofreading enzyme such as Pfu which has a much
tighter range of activity, hence less nonspecific product.