If running Receipts or Donor Acknowledgement Letters a Conditional Mail Merge may use a Conditional Field based on individual gift records or based on the Constituent record.  
If running Donor Acknowledgement Letters, check the Fields to Include Tab and confirm the correct selection is made for "per gift" or "per donor". If your conditional field is Letter Code this MUST be set to per gift.

Per gift or Per donor

If running Receipts, confirm the Constituent record on the Bio2 tab is marked for one receipt per gift if the Conditional Field is based on a field on the gift itself.  Again, if the conditional field is Letter Code, the Constituent record must receive one receipt per gift in order to meet the conditional mail merge requirement.
One receipt per gift

Once these selections are correct, click Send to the Word Merge Wizard and go through the Wizard.  Confirm the Mail Merge is set to a Conditional Mail Merge. Then confirm the correct Conditional Field is selected.  If a Donor Acknowledgement Letter was changed from "per gift" to "per donor" and saved and closed and then opened again and changed back to "per gift" this may reset the conditional field to the top field within the list, this is often Addressee.  Reselect the correct conditional field to correct the problem.