By any chance, are you using DIRECT ANALYSIS as the analysis method for the second case ( design as per AISC UNIFIED ) and using PERFORM ANALYSIS for the first case ( design as per LRFD 3rd edition ) ? If so, analysis results can vary. Otherwise if the same analysis type is used for both cases, the member forces should not change. The choice of a design code would only affect the design ( capacities, utilization ratio etc. ) but the not the actual member forces. If this does not answer your query, please upload the model and provide the details of what you are checking, so that we can troubleshoot further.
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