Mine seems to be working, v2.0.69 on a Curve, just as it's supposed to be. Under my Modules I only show one module (YahooGo) listed.
I think what they're talking about is how data is stored on a BlackBerry, there are two programming methods.
Method 1 (RMS store) is tied to the app, so when you uninstall the app the settings/data are erased. Examples: Gmail applet, LogicMail, JiveTalk (I think). This method has the ability to uninstall then reinstall an app to get a "clean" state.
Method 2 (Persistence) is not tied tot he app, so if you uninstall an app the settings/data are maintained, reinstalling "picks up" the old information. Examples: SyncJe client, YahooGo.
What Yahoo support is asking (Master Clear) is to erase the persistent data left behind after you uninstall. The only way *I* know of to do that on a BB is to uninstall, backup, erase the device and restore the backup (a backup doesn't include left-behind persistent data).
YMMV, FYI and every other acronym warnings.