wterm is an rxvt-based thing, but it defaults to using xterm for the TERM environment variable. xterm and rxvt have significantly different key controls f things like the editing keys and keypad on extended keyboards. --with-term=rxvt to ./configure would help matters a bit.
wterm-6.2.9-r2 has been added to portage currently marked unstable with a couple of changes. your configure option has been included.