It's not caused by sampling frequency.
I believe that this is due to an
incorrect number of samples per frame for ( MPeg2 || Mpeg25 ) && Layer 3
I believe that it should be 576 instead of 1152

in support_functions.h on approx. line 267

        } else if (cmp_str(bin_string, "01", 18)) {
                FI->L3 = TRUE;          
                FI->SAMPLES_PER_FRAME = 1152;
        }

should read

        } else if (cmp_str(bin_string, "01", 18)) {
                FI->L3 = TRUE;  
                if ( FI->MPV_1 == TRUE ) {
                        FI->SAMPLES_PER_FRAME = 1152;
                } else if { ( FI->MPV_2 == TRUE || FI->MPV_25 == TRUE ) {
                        FI->SAMPLES_PER_FRAME = 576;
                }
        }

-- 
checkmp3 reports incorrect song duration for sampling frequencies != 44100 Hz
https://bugs.launchpad.net/bugs/500024
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