Migration problem - do you have a solution?

[jsfitz22]

No problem - what were you going to did you write?

A couple of other questions (and if I should start a new thread, please let me know):
1) I cloned my system to a partition on the new PATA drive and about 50 files were not copied (50 out of about 20,000) - is that O.K.? I know it read that some files would not be copied (as recommended by Apple) - I just want to confirm this and know that I am O.K. going with the new system and erasing the old one.
2) I seem to have a small problem with SuperDuper! Twice now, I have set it to do certain things and once it starts copying the settings change. Here are my examples:
a) I set it to back up all files and "do nothing" after and it backed up all files and "made the new drive bootable" - also,
b) This last time, I set it to back up "newer files" and boot to new disk and it backed up "all" files and booted to the new disk.
Why won't it take my settings/commands? Thanks.