This is a confusing, but expected behaviour.
According to SequenceFile standart, each sequencefile has a sync-block, its length is 16 bytes. The sync-block repeats after each record in block-compressed sequencefiles, and after some records or one very long record in uncompressed or record-compressed sequencefiles.
The thing is, that the sync-block is some sort of random value. It is written in the header, so this is how the reader recognizes it. It stays same within one sequencefile, but it can (and actually is) different from one sequencefile to another.
So the files are logically same, but binary different. CRC is binary shecksum, so its different between two files too.
I haven`t found any ways to manually set this sync-block. If someone gets the way, please write it here.