After copying and pasting a structure into a Word 97/98 document, I notice that the text no longer wraps around the structure.
This is a Microsoft issue. It has nothing to do with ChemDraw. You will see that the same thing happens if you copy and paste ANY graphic into a Word 97/98 document. Microsoft changed how graphics are handled in Word 97/98. Support article Q167738 from Microsoft's web site discusses this issue in detail and provides solutions.
Basically, you will need to choose Paste Special from Word's Edit menu and then turn OFF the Float Over Text Option in the Paste Special dialog box.
This behavior does not occur in Microsoft Word 2000 for Windows or in Word 97 Service Release 1 (SR-1)for Windows. In Word 2000 and Word 97 SR-1, this feature behaves similar to the way it did in Word versions 7.0 and earlier. That is, the default behavior when inserting objects was changed back to inline.