Bookfile re-pagination issues

I work in publishing and we deal with bookfiles (indesign CS4) which include chapters that are non-sequential in pagination ie. colour section chapters which slot in the middle of standard text chapters.  We need to include these non sequential chapters in our bookfiles for indexing. Our problem is that despite switching off ALL automatic page numbering options ie. in the "book page numbering" options pallete from within the bookfile and within the "number & section options" pallete in each seperate chapter (where the desired page number is entered twice - under "start page numbering" and "start chapter numbering"), we still have frequent instances where chapters are automatically repaginating and continuing on from the previous chapter (and flipping from rhs to lhs and vice versa).  This issue also extends to exporting our bookfiles as a pdfs - where similar problems with pagination occur.  Looking at other forums this pdf problem at least, seems to be a common issue but the fix of saving files as IDML is not an option for us as we use a third party plugin and saving to IDML effectively strips this out. 
Does anyone have any suggestions on how to manage these pagination issues?

here is an example of one of our bookfiles.  Chapter 31-col-architiecture (pages 284-287) is a colour section that slots into chapter 32-architecture-rom7 (pages 280-294).  When this colour section is first added to the bookfile it automatically repaginates the first page to page 295, picking up from the previous chapter rather than maintaining the specified pagination (as seen, corrected, below) and throws the entire bookfile out. By doing so, it also flips the the document to start on the opposite page which has on occasion caused havoc with masterpages. Note it is not possible to physically insert the colour section into the chapter to produce a single chapter due to paragraph styles having the same names yet differing attributes (due to it being a colour section yet the content structured in the same way as the rest of the book).
our settings are as follows:
in the bookfile....
in each chapter.....
i suspect its the bookfile numbering options that arent able to be over-ridden which is the issue? 
Note that we need these files in the bookfile for both indexing purposes and cross referencing purposes, and the third party pluggin we use is Typefi which is unlikely to be the issue...

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    Message was edited by: holosys

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