We have developed a reference timing system to verify and correct the time-bases for acquired time series data. This system allows for sub-sample time registration of data acquired from separate diagnostics using heterogeneous data acquisition hardware. The system was designed to recognize and repair several types of timing discrepancies. When used as a dedicated time-reference standard, the system relaxes the requirements for cross-diagnostic data acquisition synchronization; time-bases can be unambiguously resolved from hardware that uses asynchronous clocks and triggers. This paper will describe an automated system for generating sub-sample accurate time-bases across multiple diagnostic systems on the Alcator C-Mod experiment. We will demonstrate that we can accurately determine the times of measured phenomena in order to track point of origin and propagation around the experiment. In addition, timing errors in signals can be easily flagged and corrected. The initial installation will include fast optical systems, magnetic fluctuation measurements and plasma-sampling probes. These diagnostics are distributed around the experiment cell and have disparate digitization rates.