Permissions repair repairs many permissions...why?

Question

I'm wrestling with the Snow Leopard install on an iMac 3.06. I've got the OS installed and updated along with all the other software. I'm attempting to fix printing/scanning problems now, and having not such a good time, but that's a different post.
What I'm inquiring about is this: after my every install move, I repair permissions with Disk Utility, then restart.
However, every time I Repair Permissions, I get a boatload of repairs, all from the same source: System/Library/Java/JavaVirtualMachine/...
In fact, I just ran Repair Permissions two times in a row, and it repaired those same permissions twice in a row. What's going on?

Answer 1

Barbara Daniels1 wrote:
I agree with Antonio and, I have read posts here about problems migrating from a PowerPC to an Intel machine…
That does not, in & of itself, mean there is any problem with Migration or Setup Assistant or any comparable manual method. If users migrate incompatible or damaged software, preferences, etc. from one Mac to another, then of course problems are possible. However, there is no need to worry that (for example) an Intel Mac will try to execute migrated PPC code or use out-of-date migrated cached info -- if the OS does that, then it was severely damaged by something else since these are fundamental checks the OS should perform routinely as part of its day-to-day operation.
Also, using the Setup Assistant (during the initial setup) is better than using the Migration Assistant later; although they basically perform the same tasks, the first one only sets up one account, whereas MA will sometimes create a second account with some degree of havoc to follow (this is what happened in my case; it took some time to sort it out and I won't be using MA again).
Setup Assistant will offer to migrate multiple existing accounts, just like Migration Assistant. The difference is that on the first user startup, when Setup Assistant runs automatically, there are no existing user accounts & thus no account name conflicts. Since it is not possible to merge two user accounts automatically, running Migration Assistant later, when an account has already been created on the destination Mac with the same name as an existing one on the source Mac, can result in two accounts on the destination Mac, one having a different name. Migration Assistant informs users of the name conflict before the migration begins, & gives the user several choices for what to do about it.
Some users are apparently confused by this or do not pay close attention to the dialog choice options, & end up with user files in two different accounts, each inaccessible from the other. Merging the two accounts manually can be messy, but this is true whether or not Migration Assistant is involved. The problem is the duplicate accounts, each of which contains a conflicting set of files, preferences, & other user settings in their respective home folders.