Ok let's try to pinpoint what's going wrong..
You say that "However on restarting the computer, clipbaord help+spell will for some reason "forget" the setting (even though the settings are still there) and start copying everything from that program again!"
So does this mean that the program names that you put in the ignore list are still present in the options? But CHS is not ignoring them?
If you then close the options after checking them, does it start ignoring after that?
I've written about this before, but the best solution for telling CHS to not copy such stuff to clipboard is to have those security applications properly tag such clipboard data as something that should be ignored by clipboard tools. There is a flag that has been established for this: "CF_CLIPBOARD_VIEWER_IGNORE", and according to KeePass, they should support it: http://keepass.info/news/n071012_1.09.html
Can you check to see if maybe this is disabled in your KeePass or something like that?