I presume we're talking about an Active Directory domain? How did you migrate users between servers, and did it preserve the user's GUIDs? When a Mac is bound to Active Directory, it uses a hash of the user's GUID as the unix ID number for the user (which is used, among other things, to track file ownership). Thus, if the user's GUID changes, so does their UID, and they don't own their files (and home directory) anymore. You can check this by logging in as a local user on the Mac (hopefully you have a local admin? Otherwise, this'll get complicated to fix...):
$ ls -ln /Users
total 0
drwxrwxrwt 5 0 0 170 Jul 25 2010 Shared
drwxr-xr-x+ 21 501 20 714 Feb 22 11:24 ladmin
drwxr-xr-x+ 13 875491302 759086213 442 Feb 22 13:52 fred
In the above example, the "fred" folder is owned by UID #875491302, and assigned to group #759086213. You can then use the "id" command to check the user's current UID and group membership:
$ id fred
uid=875491302(fred) gid=759086213(EXAMPLE\domain users) groups=759086213(EXAMPL
E\domain users),402(com.apple.sharepoint.group.1),62(netaccounts),12(everyone),
403(com.apple.sharepoint.group.2),404(com.apple.sharepoint.group.3)
Here, the IDs match up: fred's UID is 875491302, and 759086213 is the EXAMPLE\domain users group. If they didn't match up, you can reset the ownership to fred's new UID by running a command like:
$ sudo chown -R "fred:EXAMPLE\domain users" /Users/fred