In a calc document (Version: 6.3.1.2 (x64)) >Format Cells>Borders>Padding resets to synchronise every time the file is opened afresh.

For sheets with column(s) containing varying text content in cells the auto row height thus does not work as expected. In case an auto-filter has been applied (to hide particular set of rows) the filter has to be removed. The column has to be selected and format Cells>Borders>Padding needs to be defined every time afresh with the synchronize tick box set to off. The row auto-height behaves till something resets it back to synchronize and definitely when file is closed and opened again.

And what is your question?

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Take a look at the guidelines at https://wiki.documentfoundation.org/UserProfile to see if it can be caused by corruption in the user profile. Maybe the same with your other question.

Just tested, and no issue with LibreOffice 6.4.7.2 (x86); OS: Windows 6.1.

The file is saved as .ods?

Hmmm.

I do have to save the file to ms format sometimes but irrespective of the format the behaviour of padding synchronize being reset is consistent.

File format .xls(x) could leave behind some code that is causing this problem. If the behaviour is consistent, file a bug at https://bugs.documentfoundation.org/, and share here the number. Thanks.