Page numbering wrong when exporting to pdf

Question

I have a 340-page book, broken into about 40 chapters.  The chapters are set as the start of a section, and there are no section changes inside the chapters.  Theoretically, the pages should number consecutively throughout the book -- and they do, in InDesign 5.5.  But when I export to pdf, they get all screwed up. 
For instance, the page numbers in Chapter 6 start correctly at #27, but the following pages are numbered like this:  28, 29, 28, 29, 28, 29, 30.  The last page number should be 35, not 30.
This happens sporadically throughout the book.
I've checked to be sure each chapter has only one section, and that page numbering is set consecutively.  In ID, all the page numbers are in order.  But once they get exported to pdf, they go crazy.
Thanks............

Answer 1

Peter:  My reply above to John kind of overlaps this reply, so it might be well for you to read that, too.  You'll find there a whole list of problems I had with CS4; going back is not the answer.
I agree that one problem is that I don't have extensive experience with ID.  But I'm living on an extremely limited income, and I hoped the Creative Suite would help alleviate that.  I has done that; it has also added a great deal of frustration.  I don't have a huge IT budget to draw from.  The original outlay for CS4 was an extreme reach for me, and I didn't really have the funds for an upgrade.   How I would love to spend a few thousand dollars to fly to Pittsburgh or New York and spend a week or so immersed in an Adobe workshop!  Unfortunately, I live on a small town without such resources.  I have watched as many videos as I could find, and I have gone through several step-by-step books.  But you're right:  hands-on experience is necessary, and I'm scrambling to learn as much as I can as quickly as I can.
I would imagine you're right, too, when you say that bugs are inevitable in a complex program.  What I have trouble understanding is why they aren't fixed, especially considering the price of the program.  The problem with internal hyperlinks not working in epubs has been a known issue for some time, and according to one Adobe expert's post, the developers' attitude has been more or less, "Yep, that's a problem, all right."  But it hasn't been fixed.
Not only am I working on a limited budget, but I have made promises to clients I haven't been able to keep.  It's frustrating when clients are screaming, "Where's my book?" and I'm fighting with "known ID issues."  One novel was supposed to have been published in early October.  I was all ready to finalize it when I noticed the page numbering problem.  I feel I have spent far too much time chasing ID program bugs -- and I don't get paid for posting requests for help in the forums.
In reference to the internal hyperlink problem, I have attempted to "crack open the epub and do some fixing."  If that would work, I would have no problem; I know HTML.  But after I "rezipped" the files,  I couldn't read the result in any epub reader. I'd like to know how Ms. Castro puts its back together after cracking it open.  Perhaps it can be done with a Mac; as far as I know, it can't be done on a PC without oXygen, yet another expensive program I can't afford.   (However, after going to her website, I have decided I need to buy her book.  Thanks for that tip!)
I do appreciate your help, and I apologize for getting so impatient.  I hope you and the other moderators will be patient with me.  I'm working hard to learn as fast and as much as I can and sometimes the frustration gets overwhelming.