I ran makewhatis with both stdout and stderr redirected to a file, and yet I got a bunch of "ignored strange file name" errors in my xterm window. This is because the gawk script explicitly sends these errors to /dev/tty, which is just broken. It should use /dev/stderr.
I should also mention that the redirect to /dev/tty breaks when makewhatis is run out of /etc/cron.daily/makewhatis.cron: awk: cmd. line:54: (FILENAME=- FNR=548) fatal: can't redirect to `/dev/tty' (No such device or address)
You're right, fixed in 1.5j-3