We explore electronic transport in a nanotube quantum dot strongly coupled with vibrations and weakly with leads and the thermal environment. We show that the recent observation of anomalous conductance signatures in single-walled carbon nanotube (SWCNT) quantum dots can be understood quantitatively in terms of current driven `hot phonons' that are strongly correlated with electrons. Using rate equations in the many-body configuration space for the joint electron-phonon distribution, we argue that the variations are indicative of strong electron-phonon coupling requiring an analysis beyond the traditional uncorrelated phonon-assisted transport (Tien-Gordon) approach.