There is something subtly wrong with my Linux install that I just can't locate.

It is Ubuntu Lucid Lynx (10.04) 64-bit. Hardware is a Dell Optiplex 960: Intel Core 2 Quad CPU, 8Gb of RAM, 2x 300Gb HDDs. /home is ext2 on one disk and everything else is on the other (/ is also ext3). I have VirtualBox running a 64-bit Vista image for Outlook calendaring, but the heavyweight apps are IntelliJ, NetBeans, MySQL and Opera. Opera also loads my mail (IMAP) of which there is over 10,000 messages.

The problem is that Opera stalls for a few seconds from time-to-time. Watching the process list shows it's in log_wait_commit which means (as far as I have figured out) the filesystem is holding things up. Sometimes I can make this happen by doing a subversion update, but usually it happens for no reason I can see. It usually happens to Opera, but I've seen NetBeans go under, too. It doesn't make the app crash - it's just completely unresponsive for a few seconds.

Googling has not helped. The closest I got was to remove the sync attribute in the file system. This achieved nothing. On the advice of a Linux guru friend, I lowered /proc/sys/vm/dirty_writeback_centisecs to 300, but that didn't do anything, either. And it was all he could think of.

What is going on and can I fix it? (And how?)