Ubuntu slows down even after cpu-intensive process is ended

Question

After a Skype video call, or the use of virtualbox, Ubuntu slows down to a crawl, even after the process is ended. Running htop reveals that processes that used little CPU before are now all using about 30% cpu (namely Compiz, Firefox, Python, and Skype, but I'm sure there are others), to the point where all my cores are at 99%. All I can do from here is restart.

Any idea why this is happpening? I'm running Ubuntu 12.04 64-bit on 3.7 GiB of memory, Intel® Core™ i3 CPU M 330 @ 2.13GHz × 4, VESA: M92 graphics driver. Not sure why I'm running VESA, I installed fglrx, but I suppose that's a different question.

Thanks in advance!

UPDATE So I ran across this again after playing a youtube video and backing up at the same time. I decided to run unity --replace I received the following error:

(compiz:23601): GConf-CRITICAL **: gconf_client_add_dir: assertion `gconf_valid_key (dirname, NULL)' failed
Initializing unityshell options...done
compiz (core) - Warn: unhandled ConfigureNotify on 0xc0009e!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000a1!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000a4!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000a7!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000aa!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000ad!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000ad!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
compiz (core) - Warn: unhandled ConfigureNotify on 0xc000b0!
compiz (core) - Warn: this should never happen. you should probably file a bug about this.
(compiz:23601): GLib-GObject-CRITICAL **: g_object_unref: assertion `G_IS_OBJECT (object)' failed

So I ran unity --reset and looked into htop. It seems that a "compiz --replace", Firefox, Skype, htop, Xorg, and rythmbox were using an abnormal amount of CPU, and everything was rather laggy. Top displays the following:

top - 23:44:08 up  8:30,  2 users,  load average: 1.42, 2.15, 3.15
Tasks: 205 total,   1 running, 201 sleeping,   0 stopped,   3 zombie
Cpu(s): 29.7%us, 13.4%sy,  0.0%ni, 56.3%id,  0.2%wa,  0.0%hi,  0.4%si,  0.0%st
Mem:   3909324k total,  3713056k used,   196268k free,    78096k buffers
Swap:  4049916k total,   120360k used,  3929556k free,  2063860k cached

That amount of free memory concerns me.

Answer 1

Have a look at this page; since you are using VESA driver, I think this is your case. Check the output of glxinfo | grep render and if it says OpenGL renderer string: Software Rasterizer then this behaviour is normal until you use the appropriate video driver.