This can happen if you use old saves. Even if you start a new game because that uses the bookmark01.dat and if that one is from a previous version. So please give the MD5 checksum -- go to
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if you're using Windows -- of bookmark01.dat so we can check if you are using old saves. Without this information I can't help you further...
The patching is computational expensive, so depending on the hardware it can take some time. The latest patch is even larger and if I remember correctly the time it takes is exponential longer with size. But I see in the end it did finish. So just wait at least 20 minutes. May be in the next version there will be a progress bar, but that is a bit tricky...