http://ubuntuforums.org/showthread.php?t=1137700
This bug started for me and for others on the above thread after installing Ubuntu 9.04. Most, if not all, people with this problem are using a wireless logitech mouse (even someone back in 2005 had a similar problem and was using a logitech mouse -- see his thread at the bottom). I think it would be easiest to just copy and paste most of what I wrote in the forum:
While the mouse appears to be freely moving around the screen, it is actually getting stuck inside control objects (button, tab, edit box, menu item, slider bar, etc). The mouse cursor appears to move around the screen just fine, but when I click, nothing happens (because the mouse is still clicking inside the area in which it is actually trapped -- not where the cursor appears to be). If I hold the cursor over a hyperlink, the hyperlink is not underlined like normal and buttons that normally light up when the cursor is over them fail to do so. If the mouse is trapped in a slider bar, I can go back and move the slider bar around with the mouse and it works fine, but I cannot get the focus out of that control object by using the mouse and cannot use adjacent slider bars using the mouse. The tab key can be used to move the focus around in dialog boxes or on webpages and you can type in other fields or use the arrow keys to move slider bars around, but as soon as you click the mouse, the focus goes right back to the box or slider bar or whatever has the mouse trapped. If I click the right mouse button anywhere on the screen, the pop-up menu that would have come up if I had actually right clicked on the area where the mouse is trapped comes up with one corner of the box at the location of the traped (invisible) mouse and not where the mouse cursor appears to be. You can then left click somewhere to get rid of that box and the problem is fixed temporarily (until a few more clicks lands the cursor back in jail somewhere). The menu popping up seems to free the mouse cursor. If the mouse gets stuck somewhere where nothing happens when you right click, I can also free the mouse by closing whatever window has the cursor trapped. ALT + F4 or tabbing to a close button on a dialog box also frees the cursor. Unfortunately, sometimes you're at the desktop when the cursor gets trapped in some random area and right click does nothing and there's no window to close. In this instance unplugging the mouse and plugging it back in is a last resort and always works. This also seems to correct this problem for a very long time, instead of just seconds to minutes.
I am fairly certain that this is the same problem that most of the people on this thread are having and I am also fairly certain that the problem is that the mouse (or the mouse's focus) is getting trapped, even though it appears to be moving freely around the screen, and can only be freed by causing another window to steal the focus (like a pop-up menu when right clicking), closing the window that has trapped the mouse, or unplugging the usb cord for the mouse. Sometimes right clicking doesn't work, but using the keyboard button that does the same ting as the right mouse button (looks like a menu with a mouse cursor over it) DOES work and vice versa (not sure why).
The frequency of this problem is analogous to someone with the flu coughing. When you've got the flu, you cough randomly, but you go a few years without the flu and don't cough. This problem will not occur for a day or two and then will start happening very frequently until the mouse is unplugged. Using any other method described above to solve the problem is very temporary and the mouse will get stuck again in a matter of minutes. After unplugging the mouse and plugging it back in, I'll go for days without the problem and then it will randomly start occuring again. I am not sure what causes this to start happening. It has started occurring while using multiple different programs and even when I don't have a program open and am viewing the desktop.
This problem is extremely frustrating. I hope someone figures out what's wrong. I keep hoping the new updates that ubuntu installs are going to fix the problem, but they haven't. Logitech is a pretty common brand of mouse, so I think this bug would be worthwhile to address.
The exact same thing seems to have happened to someone back in 2005
http://ubuntuforums.org/showthread.php?t=19103
ProblemType: Bug
Architecture: i386
DistroRelease: Ubuntu 9.04
Package: firefox-3.0 3.0.10+nobinonly-0ubuntu0.9.04.1
ProcEnviron:
LANG=en_US.UTF-8
SHELL=/bin/bash
SourcePackage: firefox-3.0
Uname: Linux 2.6.28-11-server i686
I can reproduce this behavior on my Logitech MX1000 in Fedora 11 by holding down the scroll wheel button ("clicking" the scroll wheel but not releasing the click).
1. Hover cursor over e.g. an empty portion of a GNOME panel, or a launcher icon on the panel.
2. Click and hold down scroll wheel button and move cursor away from the panel, as if dragging it with the scroll wheel.
3. Right click mouse button (still holding down the scroll wheel button)
What results from the above steps is the context menu that you'd get from right clicking on whatever icon you "dragged" away from.