Hi paulstonge,
A couple background items:
1) The QIF export will export your shares up to 6 significant digits if they are in your data. If you have only 3 for a particular transaction, then it will only export 3 for that transaction.
2) The preference on how many significant digits to display does not affect how many are actually recorded. It only affects the display. Share quantities are always recorded with maximum resolution.
When you edit your transaction, you will see all of the recorded significant digits. I suspect the problem is due to rounding issues. When FM determines 'identical' transactions for filtering out, it compares the shares from the import to the existing transaction. If the absolute value of the difference is less than 0.0000005 then it considers them a match. Notice the 5 in that number is in the 7th significant digit spot.
To answer your question, the way to fix this is to correct your recorded transaction, so it doesn't have shares past the 6th significant digit. Please see:
http://www.fundmanagersoftware.com/help ... rrors.html
If this doesn't resolve the problem, please let me know. Some specifics on the particular transaction share quantities in FM and in the QIF would be helpful.