I often come across the same problem with inexperience users on 4chan's /f/:
They don't seem to understand that there are multiple site domains (because it's rather unusual) and, even when I never had that problem, probably did not read the site architecture at all.
What I'm trying to say is, they don't know how to search for keywords in archived threads.
I think the reason is that the second search button for the .net engine isn't clearly visible at all.
Maybe this was intentional. But if I would not have been on swfchan on older layouts, I probably wouldn't know about it as well. I remember having to figure it out a little bit myself.

Most visitors probalby only visit the frontpage and don't immediatly recognize two different search functions.

My suggestion would be to put it back to two distinct buttons (maybe "Search", "entry field" and then "flashes" and "threads" as buttons - maybe even differently coloured).

Just wanted to throw this in, thanks for attention Ants.

But you're right, the function should be more clear to people that it is there. I've added a "Search for keywords in threads instead?"-link that is shown for all searches on .com, that way people will still start out with the search that they most likely want to perform but will become aware that there's another way for them to find what they are after. Hopefully that is enough.

Thanks for pointing this out to me, something should should have been done about it back in April of 2014 when swfchan's server got a big upgrade.