Since upgrading to OS X 10.6 (Snow Leopard), I’ve been frustrated by Terminal’s focus follows mouse behavior. I typically like such behavior but it’s broken as of 10.6. I would frequently CMD-Tab to switch to a different application and start typing only to wonder why my keyboard was not working, then realize my input had gone to the Terminal which sometimes was no longer even visible.
To fix this, type the following in Terminal:
defaults write com.apple.Terminal FocusFollowsMouse -string NO
Then, restart Terminal. Voila! No more lost input in my Terminal.
Many thanks to www.macosxhints.com for popping up when I googled this problem.