Pagination woes

Hi - wonder if anyone else has this problem...?
I have three Framemaker book files. To simplify (and reduce the number of files, let's say I have:
* Master book file
file a
file b
file c
file d
* Book 1
file a
file b
file c
* Book 2
file a
file b
file d
Some files contain conditional text. I have set each file (independently) and each file in the book, apart from file a, to delete empty pages, and start on next available page. I have a double-sided layout. I display *all conditions* in the Master book before selecting Update Book. I then open (say) Book 1, display *its* conditions and choose Update Book.
My problem is that, no matter what I try, whenever I try to build Book 1 or Book 2 the pagination does not work correctly.
I always have to go back through individual files after updating, and re-apply the correct Master pages, when they should update correctly/automatically. This is a pain, as my real books contain many files (not just 4 as above). Specifically, a chapter page will start on the wrong side, and/or an extra blank page will be generated at the end of a file.
When updating, I select "Apply Master Pages", and have the following Master Page assignments on the Reference page:
UnstructMasterPageMaps
Book Update (Yes or No): Yes
Paragraph Tag Name    Right-Handed Master Page (or Single-Sided Master Page)    Left-Handed Master Page    Range Indicator (Single, Span pages, Until changed)    Comments
Chapter.number    First-R    First-L    Single   
Appendix.number    First-R    First-L    Single   
IX.name    Index-First-R    Index-First-L    Single   
TOC.name    First-R    First-L    Single   
Glossary.name    First-R    First-L    Single   
Manual title    First Front        Single  
Regards,
Martin Ley
martin at em-dash dot com

Hi Art,
Thanks for the speedy reply.
I'm using Frame v9.0p250 under XP SP3, itself under Parallels Desktop for Mac on my MacBook Pro 17", 8GB RAM, OS X 10.6.2.
I thought I had covered all pagination eventualities by saying "I have set each file (independently) and each file in the book" - maybe I wasn't explicit enough - apologies. What I did (as well as going into each individual file and doing it) was:
1. Select the first file in the book (actually from the Book file) and set Pagination to Double Sided, Right, Delete Empty Pages.
2. Select all the other files and set Pagination to Double- Sided, Next Available, Delete Empty Pages.
Knowing that book settings stomp over individual file settings, I figured that was the way to go.
I suspect that you may be correct when you talk about my specific requirements throwing off the automatic pagination. The weird thing is sometimes it works if I update twice in a row. These manuals have been in existence since Frame 5, and I have 'improved' them many times over the years. Perhaps this page layout is a bridge too far - I was hoping the Reference page setup would work for me - it seems that's what it's designed to do (applying specific Left or Right masters depending on paragraph tags).
Again weirdly, I thought I had solved the problem by not having the 'master' book open at the same time as the 'conditional' book. I considered this because I was getting another problem:
1. Open both book files.
2. Open all files in the 'conditional' book (i.e. a subset).
3. Page through the files in the conditional book to check pagination (due to problems above).
What happens is Frame asks if I want to open 'the next file in the book'. No - I already have all the files I need open, but Frame assumes I'm using the 'master' book, not the 'conditional' book. Bizarrely, in a previous installation (before TCS2) I was also getting pages that would be hidden after updating - they existed in a file, but I couldn't turn the page to see them! I forget how I solved that one, but I suspect it was part of the same problem. They were always the last page in a file.
In fact, after my initia euphoria, I discovered that only having one book file open did not solve my pagination problems - it was updating for a second time that had solved them (sometimes). I haven't tested this exhaustively (sometimes, manually repaginating means I actually get my work done instead of fuming over what I think should be happening but isn't!). I have a bug logged with Adobe support, but I suspect I will have to reinstall Frame if I take their back-to-first-principles solutions. No thanks. I lost faith in tech support a long time ago.
Hope I haven't muddied the waters too much with my extra explanations. I was trying to keep it simple first time around...
Regards,
Martin

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    281  bytes received via SQL*Net from client
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       4 - filter(ROWNUM<=1200)
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              1  recursive calls
              0  db block gets
            348  consistent gets
              0  physical reads
              0  redo size
           1063  bytes sent via SQL*Net to client
            385  bytes received via SQL*Net from client
              2  SQL*Net roundtrips to/from client
              1  sorts (memory)
              0  sorts (disk)
             11  rows processed
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              0  db block gets
            343  consistent gets
              0  physical reads
              0  redo size
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            385  bytes received via SQL*Net from client
              2  SQL*Net roundtrips to/from client
              1  sorts (memory)
              0  sorts (disk)
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    Execution Plan
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    |   0 | SELECT STATEMENT               |       |  1200 | 91200 |   179   (2)| 00:00:03 |
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              0  physical reads
              0  redo size
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    Check out my APEX-blog: http://inside-apex.blogspot.com

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