The problem is with vte (the terminal widget that gnome-terminal uses). A feature was added that sends a number of up/down keystrokes instead of regular scrolling if it is using the alternate screen or scrolling is restricted (one or both of which are the case when using ncurses applications).
I wrote a patch for vte to make the feature toggle-able, and a patch for gnome-terminal that allows you to turn it off or on for a profile. I filed a bug for this at:
You can get the patches there. Unfortunately, it looks like the vte developer isn't very receptive to the idea of making the feature configurable, which is kind of baffling to me.
The gnome-terminal patch makes the setting available under the "Scrolling" tab in the profile editor.