I think that's a libvte pecularity (used among others by the Gnome and XFCE terminal emulators), which upon entering <clear> (or pressing CTRL+L) just scrolls up until the screen seems to be empty. Make sure you set terminfo correctly, ie. E3=ED3, so that it clears the text and scroll buffer.

On any non-libvte using terminal emulator, eg. xterm, you can use CTRL+L to clear the text area and ALT+CTRL+L to clear the text area and the scroll buffer.