Problem with function keys while using Terminal to connect to UNIX host

We are trying to use macs at my office, but we've hit a big roadblock. Our company software runs on a UNIX server, and until now everyone in the company uses either dedicated UNIX terminals, or terminal emulation software in windows. I was thrilled to learn that we could use the terminal in OSX to connect to the server, and it did not take long to get it to work.
The problem is the function keys. Almost all of the menu options in our company software require the use of the function keys, F1-F10. I was able to access F9 and up by pressing command-F9, etc. but we're now having issues with F3 and F4.
The computer in question is an intel macbook, and we have been using the fn key of course. The specific problem they showed me was with F3. In the software, it is supposed to lauch an extra menu, but pressing fn-F3 on the macbook results in an error ("number required", which is the message it would normally return if we tried to press return).

Your problem is two-sided, I think. The first is that you need to set Terminal to send the right escape sequence. This is done with the Inspector (CMD-I) and selecting Keyboard. Get the correct key mapping in there. The other side is to make sure the system isn't intercepting your intended keystroke, so go into System Preferences->Keyboard & Mouse->Kwyboard shortcuts and make sure that the bindings you're using aren't enabled.

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