IIRC whenever you use the loadvariable/savevariable command, Fungus addends the current profile to the key automatically (to let you load/save into different "profiles" by default). This does have the effect of not letting you automagically load any playerprefs value. You could however quite easily create a custom command that just calls the default SetString/GetString (or whatever) PlayerPref commands for your own keys outside of Fungus. You might also be able to extend the save/load variable command to let you remove the added profile stuff and just load/save keys directly.
Thanks as always, Wolfrug! I'm never going to need or save to more than the one profile, so the way that I solved this was to actually do it backwards - I redirected the *non*-Fungus systems to use the Fungus-created, underscore-appending key instead. If anyone else is seeing this and not planning to use more than one profile, this is probably a simpler option. A big 'ol find-and-replace through all of your scripts that changes the key name to what Fungus calls it and you should be all good. :)