PDF export to version 1.3 results in unexpected results

Question

Using InDesign CS5.5 - and Acrobat X - Exporting to Smallest File Size, changing to PDF 4 (1.3) [instead of the PDF 6 (1.6)]
As always I choose Smallest File Size for the Web.
I selected Acrobat PDF 4 (1.3) and then some text went off the page ... but only on one page.. (FIGURE 2)
And on another Page the text was also duplicated on the running head from the opposite spread. (FIGURE 1)
I then tried the PDF Print Settings that I ALWAYS use - which is to Flatten the Transparency (see Figure 3)
The Text Shift is now happening on TWO pages - and also the Running Head is duplicating on TWO pages now too - it's even worse than Web PDF.
I need to Flatten the Transparency in these PDFs - simply because I need to, don't really need to go into details. I don't see how Flattening or leaving live transparency could affect the position of a text frame anyway?
Any ideas?
Figure 1
Figure 2
Figure 3

Answer 1

After a few rounds of testing various things:
I applied a Master Page of None to all the pages - and the pages exported correctly.
I reapplied all the master pages to the various pages as needed. And again it exported incorrectly.
I deleted all the Master Pages - recreated them and reapplied them - and it's all working as normal.
Cause seems to be some sort of corruption with the Master Pages.