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This was present in 3.5.1 and is still present in NB 3.6. If you modify the value of a cell in the property editor, and select ctrl-s while the cursor is in the same cell, the value is not stored. You have to move the cursor to another cell for ctrl-s to save the value in the cell you edited. The same goes for the value box in the editor. Also, the file icon is not badged when it is not saved.
*** Issue 40978 has been marked as a duplicate of this issue. ***
Confirmed. It happens with NetBeans 3.6, too.
*properties* is the right component.
Fixed. Ctrl-S should work by now.