Your conclusion is correct. I have exactly the same problem in my project. I think, that this is an undocumented use of bit 6. The solution is easy: just mask the unused (and for that reason uninteresting) bits and you will see, that the information is still correct. But I agree, that it is strange, and nowhere on the Philips site you can find any comment on it.

The most strange thing is, that this indeed always happens for a seconds value of 40H .. 59H and not if seconds is within the range 00H .. 39H. Also bit 6 of register 01H shows this behaviour, even while in the datasheet is written, that bits 7, 6 and 5 of this register should contain always 0!

Greetings from Holland!