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The middle mouse click used to work fine for me, but for some reason, now it's very tempermental. Sometimes it will work with aterm and other times it won't work at all. No matter how I copy the text I want to paste, sometimes nothing will be pasted in an aterm instance. It's bleeding annoying. I can still paste to xterm, but not to aterm.
I'm having a similar problem: my copy-paste using middle mouse button doesn't seem to be active in Firefox--works just fine in other programs (select to copy, middle-click to paste). However, copying out of or pasting into, or doing either entirely within Firefox, seems defunct. To copy anything out of Firefox, I have to select it, hit ctrl-c, and then I can paste elsewhere with middle-click. I'm running Debian Sarge, with Firefox 1.0.1-2 installed via apt-get. This used to work on this computer, and still does on my laptop (same distro).
Is there a way to cut or delete things quickly? I find the middle mouse button useful, but I also think ctrl-x and generally having the keyboard available is useful when you aren't near the mouse or your hands are very busy on the keyboard.