Did you double-check, if the "Log visits" option under the home directory tab is enabled?
Compare the NTFS permissions of the folder which work to the folders that don't work. Maybe there is a missing permission. But you should see some evidence in the Windows Server eventlog for that issue.
There is a Microsoft TechNet article which could help: Troubleshooting Logging Problems (IIS 6.0).
Some of IIS 6.0's settings can be set "globally", like the default start path of the log files. See this article on TechNet:
Changing Default Web Site Settings (IIS 6.0)
However, some of the settings you change will not affect your existing webs. For example, if you set the default path for your log files, this won't change the folder for your existing log files.
During IIS installation, default
values are set for the various
properties assigned to Web sites.
Properties can be set at the global
level, affecting all Web sites on a
server, on the individual site level,
at the directory level, or at the file
level. IIS uses an inheritance model,
which means that settings on higher
levels are automatically inherited by
lower levels. Settings at lower levels
can be edited individually to override
inherited settings from the next level
up.
If you change a setting at a lower
level, then later change a setting at
a higher level that conflicts with the
lower level setting, you will be
prompted to choose whether you want to
change the lower-level setting to
match the new higher-level setting.
Regarding the home path of new web site: if you create a new web site, the IIS wizard will always prompt you for the path.
If you have to migrate your files to a new folder, I would do it one-by-one (if you don't have hundreds of them - then some scripting would be necessary). Be sure you test the sites and check if there are directories which needs "special" permissions.
Best Answer
Microsoft have details here but the summary is:
Go into the registry and amend
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\HTTP\ParametersCreate a String calledErrorLoggingDirand point that somewhere else. Don't include theHTTPERRpath, as the HTTP service will create anHTTPERRsubdirectory anyway.Then you restart the HTTP service (net stop HTTP, net start HTTP) and then start any dependent services - eg W3SVC. The HTTP service (http.sys) does not appear in the services MMC, so you have to use a command line to start/stop it.