I Googled it and found a bunch of people had run into the same issue.
There are a bunch of files and directories that are normally excluded from backups - which are contained within the following plist files (You can see them just using a text editor or Quickview or edit them using e.g. Property List Editor) - check the 'ExcludeByPath' keys:
Note: That in the com.apple.TimeMachine.plist there are a bunch of items that get added by certain Applications; Xcode adds the directories named 'build' (and maybe others) to the list exclusions, and Google's Chrome adds it's 'cache' directories to the exclusion list. There's probably others out there as it is achieved using a standard API call.
You can also find, using mdfind the OSX's command line version of Spotlight, all files or directories that have had the appropriate metadata attribute set (using xattr command) for backup exclusion:
sudo mdfind "com_apple_backup_excludeItem = 'com.apple.backupd'"Out of interest you can list the metadata attributes on any file/dir:
mdls /path/to/that_curious_fileHowever in my case none of the above applied and it seems that under Sow Leopard there's some 'bug' that stops TM working properly if you haven't rebooted in a while (which I hadn't). So a simple reboot fixed it?! Not reassuring though.
There's a good list of things to check here and there.