Have you had this MDD for very long… as in - are you aware of its’ operational history? Any new hardware attached internally or externally? (New PCI cards, network connection, video, etc.?)
Best practice when installing a new or fresh operating system is to take the machine down to its’ barest bones before the install: mouse, keyboard, video card, period. No unnecessary peripheral or external devices (or network) connected during the install and then add them back, one by one after the install, testing each one AS you add them back, for any problems as you go. Omit the KVM switch and only add it back after all else has “tested good” and stable.
And did you re-initialize / format / partition the hard drive with Drive Setup 1.9.2 or Drive Setup 2.1 before this fresh installation? Is it the original HD and no other HDs are present inside?
But perhaps even before all of the above… download, burn to CD and run Apple Hardware Test for the MDD. AHT Version 1.2.7 from here:
http://macos9lives.com/smforum/index.php?topic=822.0 And then run it again perhaps, even after another “fresh” installation… even if everything checks out good with the installation.
AND if the condition of your current HD is that questionable (or especially tests questionable with AHT) there are many SSDs and suitable adapter bridges that are now very affordable and can easily boost performance and dependability.
Of course you might also
try simply rebuilding the desktop AND or a PMU reset too. But I would definitely run AHT - regardless.
Stay tuned, others here might have other suggestions like "Blessing the System Folder". Good luck!