Here's what we did to resolve the issue:
Go to Confluence Administration -> Add-ons -> the two Play SQL plugins, and check all modules are enabled,
It wasn't enough, so Peter disabled and re-enabled the plugins.
Note that it's also possible uninstall/reinstall the plugins, as the data persists across reinstallation.
Confluence 5.3, MS Internet Explorer 9, Windows 2003R2 (server), Windows 7 x64 (client)
Upgrade to version 2.1 and none of your playsql query macros are recognised (both legacy and new query ones)
In the Plugins there are now two Play SQL ones, (Play SQL and Play SQL Base)