I have a similar issue to another user who posted to this site about figure caption numbers not converting properly.
I created captions for each chapter of my document (ex. Figure 1-1, Figure 1-2, Figure 2-1 etc). This document has been modified a number of times over the past 2 years, figures added, removed etc. When I add a new figure in-between other figures and then add the caption, the auto-numbering is off; it's as if some caption numbers are hidden somewhere in the document (ex. Figure 3-4 follows Figure 3-2 (why doesn't it auto-enter Figure 3-3?)). As a result, I have to manually enter the correct number. When I convert the document into PDF, the numbers do not convert exactly as entered in the Word document.
Read in your other post to see if the numbers appear properly when you print preview the document. They do not. How can I fix this so that the numbers appear properly in my Word doc so that they convert properly in PDF?