Disk Utility: Extremely slow read phase during permissions repair

Question

Shortly (but not immediately) after I upgraded from 10.3.9 to 10.5.6, repair permissions began taking a ridiculously long time to complete. Looking at the DU log, I see the read phase is the problem: DU spends over 2 hours on this, then performs the repair phase in a reasonable period. I'm using roughly 90 of my drive's 150 GB.
Last night, in Activity Monitor, I saw DU start 4 threads, which used 3-5% CPU initially. Checking later, I noticed CPU had dropped to 0% and stayed there until the repair phase started, at which point CPU went to 3-7%.

Answer 1

You know, don't you, that "Repair Permissions" doesn't actually REPAIR anything?
It does one thing: It goes through the BOM file (and, now with 10.5, the database as well), and compares the permissions on system files and on applications installed that put a receipt in there, and RESETS the permissions to whatever the BOM files and database say. Nothing more, nothing less. NO ISSUES related to the users home folder can be repaired in any way, because there are no receipts for them.
I'm not saying there aren't a set of very specific issues that "Repair Permissions" can't fix. But to say it should be regularly used to troubleshoot and as proactive maintenance is like recommending chiropractic care to fix a hangnail. It probably does more harm than good, as there may be cases where you actually WANT to change permissions, and "Repair Permissions" stomps all over them.