Things to remember regarding saving settings:
1) Unless you first configure your GLOBAL settings, you will have to configure every network individually. This is one of the most common reasons people think the settings are not being saved. To configure GLOBAL options (the settings that remain the same for all networks), make the changes while you are not connected to ANY networks.
NOTE: If you have already run Invision after installing it (or if you imported files from earlier versions), the GLOBAL settings are only going to affect networks you have not yet been to. All other networks that you have been to have already had their settings created using the previous GLOBAL settings (which are probably settings you don't want because they are the default settings and not your own). GLOBAL settings are the default settings that are applied to a new network before you make individual changes to it.
If you are having problems with your GLOBAL settings not being what you wanted and you've been to other networks, you may want to reinstall Invision and do NOT import any settings, or you can go to your mirc\Invision\Settings\ folder and delete all folders in there while not connected to any networks. Then you can edit your GLOBAL settings. The new settings will then apply to all networks until you make changes for a specific network. Be certain that you set up every setting that you want to be GLOBAL before joining any networks.
For further help on GLOBAL settings, just ask.
2) Save your settings every time you make any changes.
3) If you have problems with your computer crashing, you should close Invision after making any changes. Even if you save your settings, if Invision crashes (or your computer does), you will lose any settings you had. By closing Invision, the settings become permanent (unless something else happens to them -- you make changes, delete files, etc). NOTE: This may be different in the latest build as I've not tested it yet... but in 2520 and earlier, this was the case.
4) Regarding multi-server. You WILL lose settings, guaranteed, if you connect to the SAME network more than once with Invision. You should have no problems connecting to multiple DIFFERENT networks, but by connecting to the SAME network more than once, you will lose your settings for that network (I believe they return to your GLOBAL settings). NOTE: This doesn't mean just the same SERVER, but the same NETWORK. (i.e. You can't connect to different Undernet servers without problems... only to completely different networks such as Undernet and Dalnet).
For any questions about these things, let me know.