I'm running samba 3.0.31 on Fedora Core 8 x64 that compiled using samba-3.0.31/packaging/RHEL/makerpms.sh.  logon scripts are not being loaded automatically.  As an example I created a user jdoe and his LDAP info has:

sambaProfilePath: \\roark\profiles\jdoe
sambaHomePath: \\roark\jdoe
sambaLogonScript: scripts\jdoe.bat
sambaHomeDrive: R:

and when I log in as him, using a Windows XP Pro SP3 computer, he gets R:, but his jdoe.bat isn't ran which is:

net use s: \\10.8.16.2\share /yes
net use m: \\arrowhead\hppictures /yes
net use p: \\arrowhead\public /yes
net use v: \\arrowhead\archist /yes

when you look in "my computer" he's not shared any of those drives.  However, if i click start, run, and type in \\roark\netlogon\scripts\jdoe.bat the script runs fine and he is shared those drives and now they show up in "My Computer".

At the URL above ( http://www.mdah.state.ms.us/samba/samba.zip ) it is a zip file containing jdoe and jdoe$ LDAP info, my smb.conf created with testparm, and a log level 10 output from when I joined jdoe$ to the domain, logged in as him, saw that he didn't have his netlogon script ran, and logged out as him.  I did not manually run \\roark\netlogon\scripts\jdoe.bat as him but know it works for all other users and I've had to place a shortcut to their login script in their startup folder as a work around.  I can provide a log level 10 of running \\roark\netlogon\scripts\jdoe.bat if needed.