This problem occurs when the column mode is activated.
To reproduce, simply follow those steps :
1- Create a text file
2 - Enable the column selection mode
3- make some modification
4- Save the buffer, the file becomes unchanged
5- using the mouse, click somewhere in the file and the buffer becomes unsaved.
very anoying...
Thank for the fix !
In the User's Guide ( http://www.jedit.org/users-guide/selection.html#rect-select ) You will find this hint:
... if keyboard rectangular selection mode is on ..., clicking beyond the end of a line will insert the appropriate amount of whitespace in order to position the cursor at the clicked location.
So, You've found a feature ;-)