Permission right issues after restore from TM (disk utility doesn't help)

o my hard disk crashed and when I installed the new one I tried using the setup program to restore my mac settings from my Time Machine backup. But for some reason the process continued to freeze halfway.

So I ended up having to use the migration assistent to restore my "user settings" and setting the other stuff back manual from my Time Machine backup. (any restore smaller then 10 gig seems to go smoothly, larger ones seem to freeze).

I had to reinstall iTunes which was no biggy, but after I did the major updates I started having permissions issues. The 2 that I came across so far are the next:

1) I don't have any acces to my "Download" map. It says that I can but items there but I won't be able to see or use them because I don't have the right access rights. (It also says other users might, but I am not the only user ...)

2) when I start up Adium the program tells me it can't make the right maps to save login information etc and suggests that I use "Disk Utilities" to correct it. (So I can't save my login in formation)

3) Some maps have a red no access symbol

I have been running the Disk aid program to restore access right but it doesn't seem to resolve these issues.