How do I move a page or delete a single page in CS6 indesign are keep format?

Question

  I created a 75 page book in InDesign CS6. The template had double-sided right and left facing pages, each with a black border and page number in the center bottom of the page.
As an experienced InDesign user, I had very few challenges putting the document together. Once completed, I edited the images and attempted to rearrange some. I traded some even numbered pages  with odd numbered ones. I added a few pages and deleted others. Then I discovered that many of the pages were not formatted correctly. Numbers were no longer in the center. Borders framed only 2/3 of pages, shifting right or left onto the pasteboard.
After careful study, I discovered that everytime a single page was moved, all the subsequent pages were formatted incorrectly. If two successive pages were moved together, formatting remained appropriate.
I called Adobe for support. I called over and over again. The first level of support required me to describe the problem. The low level support was repeatedly stumped.  After considerable time on the phone, they escalated the case and told me someone at the next level would call me back within 72 hours. This happened 3 times. I was never called back within 72 hours. I was called back a week after my third call when I was several hundred miles from my computer and the nearest WiFi. I was given yet another 72 hour window in which I was supposed to sit by my phone and wait for a call. Again no one called.
I called again and again. I explained my problem over and over. At this point, after being cutoff three times this afternoon and once this morning, I have come to the conclusion that not only does Adobe have no way to solve this problem, they lack the courtesy to tell me so. 
I am using a Macbook Pro, previously with 10.7+ and now with system 10.8+. The error is clearly in the program. I have a clumpsy way to do what I want but I can only put in page numbers page by page.

Answer 1

https://www.dropbox.com/s/74iqzfbqj8r01v7/indesign%20problems%202-3.jpeg
This link shows the document as it originally was.
Next I switched page 2 with page 3. (so 3 comes first).
https://www.dropbox.com/s/pvicu6zvr87j5tz/indesign%20problems%203-2.jpeg
This link shows a page from a longer document and the misplacement of Master page set-up. Note that some pages have correct border and number placement while others do not. The border extends beyond the page onto the pasteboard.
https://www.dropbox.com/s/ade4580gx0lleyd/document%20with%20several%20incorrectly%20format ed%20pages.jpg