microsoft word equation vertical alignment and display font sizeissue

In Microsoft Word 2003, when I add a new inline equation into a large
word document (50+ pages with tables, equations), the equation
vertically aligns with text around it well, i.e., bottom aligned.

Overtime, this document grows so huge, that I'd like to either copy
paste the entire document into a new document, or save it as a new
document, to shrink the file size, and prevent frequent crash of word.
But either way, in the new document that I created, or saved as, all
equation now shows up slightly smaller than it is in the original
document, and it sits slightly higher than the text around it (when
looking at the bottom of the equation and the text).

If I double click the equation, going into edit mode, but don't make
any change and go back to word immediately, then the equation displays
normal again, i.e., the equation font now looks normal (same as it was
in the original document), and vertically align well with text around
it.

This is office 2003 professional on Windows 7. But I believe this
problem appears in multiple versions of word (2000, XP), and on both
Windows XP and 7.