Hmm, that's odd.
I have the Linux edition, and also downloaded the eob_2_clue_book.zip from the bonuses list. In my case both the standalone copy of the cluebook as well as the one installed in the docs subdirectory under the game, in the page 7-12 range, go as follows:
7, 8, 7, 10, 9, 12
In other words, page 10 is there, page 9 is in the wrong order, there are two copies of page 7 and page 11 is missing altogether.
The cluebook PDFs are scans of the original physical clue books from SSI, and I'm not surprised to see such errors occasionally crop up (earlier printings of the Secret of the Silver Blades cluebook, for instance, had two copies of the map of the 1st level of the mines and were missing the map of the 3rd level, which had to be provided on a yellow errata sheet, and I recall mention that the GOG edition of Secret also had this error at least initially - it's not too far fetched to imagine that the EOB2 cluebook had such a printing error at one time as well); however, it seems odd that it would crop up in two different ways like this (as you indicate you're missing *two* pages altogether) ...