I use tiddly wiki, which is a local wiki engine. When I have multiple layers open and try to close all, the tiddly wiki will ask me for confirmation because it hasn't been save. I pressed cancel but all pages are closed anyway. This seems to be a wrong behaviour.

In K-Meleon you have this option to configure this:
Edit -> Advanced Preferences (F2) -> Browsing section -> Layered Browsing tab ->
Confirm closing multi-layered windows.

This option only work, ask you if you really like close all tabs, if you close window with next actions:
- Click over up rigth square close button (X).
- File -> Close Window
- Alt+F4

Are you tried if this happend with others browsers?
This can be a tiddly wiki bug, are you tried to change User Agent string in K-Meleon to Firefox or IE, for example?

K-Meleon in Spanish

Thanks for the reply. I tried both but neither worked. Actually the confirmation dialog tiddly spits out before closing asks me whether I wanted save it. If I press OK, it does save the change. It's just when I press Cancel, all windows get closed, while on Firefox, the "close window" operation was cancelled.

Are you tried with JavaScript Enabled?

K-Meleon in Spanish