In my experience it's actually rarely used negatively (ymmv of course) - I only really hear it when the context is "these people (the boffins) do something abou

In my experience it's actually rarely used negatively (ymmv of course) - I only really hear it when the context is "these people (the boffins) do something about which I don't understand", so it's almost self-deprecating to call them boffins. On the otherhand it's also not particularly positive, either. As an example: Stephen Fry uses it, and he is a.) a geek and b.) not the kind of person to insult people for that kind of thing - when he uses it he always just means that they're people doing something complicated that he doesn't know about.