Usually, when you first create a book and start adding the .indd files to it, the pagination is automatic. I don't have CS5.5 but I'm assuming it's similar to ID CS6 on this regard. If you select an .indd file in the book panel and check Document Numbering Options, do you see Automatic Page Numbering selected? What do you see on Start Page Numbering at?
Under Document Numbering it says automatic and under Numbering Options i have Continue from previous document and Auto update page numbers and section numbers checked.
In your screen shot above, on the left side (the book file window) my numbering appears as:
Chapter 1 1-35
Chapter 2 1-8
Chapter 3 1-4
None of the chapters in that window have consecutive numbering.
In the screen shot on the right, my file DOES have "automatic page numbering" checked. The starting page numbers, however are not correct. For instance, chapter 2 may say staring number 6, but chapter 3 says starting number 4.
The good news is, that all the pages appear correctly now when I save the book for epub. I would still like to know why my book file windows are not correct, but ultimately, the ebook is the main thing that needs to be right.
Why don't you try creating a new book file and add your .indd files to it.
I have started over 5 times. I even used different (unrelated) files to see if my chapters were corrupt somehow.
I got the same result every time. I think the pages seem to BE paginated correctly—just the Book window is wrong (since I am doing an ebook—there are not physical page numbers).