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...it's probably something REALLY simple!

It's likely some algorithmic thang. Entering a new note, the note length of the previous note seems to get shortened by some percentage - which shortens a whole note by a larger absolute amount than a half note, say. Thus keeping the tie with half notes and jettisons the tie with whole notes.

You may easily keep your ties, if you enter s.th. like '90' into the field 'Duration%' of the dialog "Notation Window Options/More -> Other Notation Options/Inserted Note Defaults".

Martin