Some groups have default configurations. For example you might not be aware of the game binding the tertiary trigger to the large port occasionally. Weapon groups are weird.

Mission notes are saved when you quit the game. You must use the Quit button on the login screen for them to properly save. Any kind of force exit or other improper kill of the game will result in it not being saved.

It sounds like your problem is a misunderstanding of how weapon groups work. When you don't assign any weapons to the Tertiary trigger of group 3, what happens when you switch to group 3 is that the weapon assignments for the tertiary trigger don't change (as opposed to removing the weapons that were previously assigned to the tertiary trigger like you are expecting).

So with the following setup:
Group 1: neutron blaster on primary trigger, large port rockets on secondary
Group 2: primary blank, scanner on secondary

Switching to group 2 changes the secondary trigger to the scanner but leaves the primary trigger unchanged. Thus you would have the neutron blaster on primary and scanner on secondary.

See this thread for more info:
http://www.vendetta-online.com/x/msgboard/1/28902

As for your missing mission notes problem, that sounds like it could be a file permissions problem or that you are running the vendetta client from a write-protected volume.