soundconverter failes to convert from ape to flac in most cases

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When converting Monkey Audio APE-files to FLAC, it seems to do the job. But when you try to play newly converted FLAC-files you probably get jagged sound or even no sound and stream decode error. I noticed that duration of stream is not the same as in input file.
I have found no such problems with ogg -> flac or ape -> ogg.
System: Ubuntu 8.10 x86
Package: soundconverter

Steps to reproduce:
1) Open Sound Converter
2) Add ape file
3) Set in preferences dialog "Type of result?": flac
4) Convert
5) Open newly converted file in totem
6) Even if it seems normal, try to seek through file and look at duration in status bar