MP3 Decoding Discrepancy
It is possible that two decoders will have different results and be compliant with standard. The standard "ISO/IEC 11172-4 (part 4) compliance testing" specify two classes of decoders: 
"accurate" and with "limited accuracy" *). 

The accuracy is measured by comparing decoded stream with reference stream (reference input and output is specified in standard). If the RMS of difference is below $2^{-15}/\sqrt{12}$ the decoder is classified as accurate and  if below $2^{-11}/\sqrt{12}$ it is classified as "limited accuracy" one.

So if you are going to use different decoders or even the same decoder on different processor architectures you have to be prepared for this kind of discrepancy in output. Do not know your application or intend but maybe you can mimic the standard and work with RMS of error too?

*) I do not have text of the standard in English in front of me so actual name used in standard may be different.