In the absence of any solutions from the list, Time Machine solved this problem.
It would always be interesting to know how or why something happened. May have been a fonts issue. I don't know.
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I have just reinstalled 10.6 and updated it to 10.6.2. I ran permissions repair again and it now repeats less text than before, but it still does not appear to repair the permissions and when I run the application again it displays the same list of repairs.
CS3/4 now says "Licensing for this...
For 2 days my permissions won't repair completely. I run the repair - it takes 20 minutes, examines every file on the computer and ends. When I run it agin it does the same.
CS3/4 suite, Max/MSP, all crash. MS word will not open. Apple software OK.
17" MacBook Pro 3.06, 250 G solid state...