A few observations. Are your filesystems journaled. They say ext3, which IIRC does support journaling?
the flashplayer should not be able to trash the file system. /var/log/syslog is a place to look for io errors. If you are having them you likely have a failing disk and need to replace it ASAP. given the cost of disks, running raid 1 with pairs of disks is really a good idea. When one fails you pull it, replace it, and rebuild, all without data loss or loss of use of the system.
