The most likely cause of this is that the custom field is mapped to the Member ID field. To fix this:
  1. Navigate to Fundraising, Donation Management, All Donation Forms tab
  2. Find the donation form in question
  3. Click Edit from the Action column
  4. Go to Step 3. Design Donor Screens
  5. Edit the Donation Form
  6. In the "Arrange the order of the selected data elements" column (right side), click on the element that contains the custom
  7. Click Save Order and Edit Selected
  8. Scroll down to the Edit Data Element section
  9. Click "Edit this element type selection"
  10. In the pop up window, scroll down to Step 4. Update Contact:
  11. Choose a different field to have the custom field mapped to
  12. Click Apply
  13. Click Save