Neuralynx acquisition software, Cheetah and Pegasus, save data in several different formats.  These formats depend on the type of acquisition entity you are recording, and include:  .nse (single electrode), .nst (stereotrode), .ntt (tetrode), .ncs (continuously sampled), .nvt (video tracking), .nrd (raw data), and .nev (events).  

CSC (.ncs) files are formed from 512 samples.  The timestamp is on the first sample of that record.  This occurs regardless of the sample rate.  If recording at 32kHz, each record of 512 samples is 16ms.  If subsampling down to 16kHz, then each record contains 32ms of data, but still with 512 samples.

Spike files (.nse, .nst, .ntt) are made up of 32 samples.  Each will contain a 32 sample data structure X the number of electrodes.  The same rules apply here as they do with CSC files and subsampling.  
The timestamp of spike records is on the alignment point set in Cheetah, typically the 8th sample.

Event (.nev) files timestamp each event input from either manual input from the Event Window/NetCom commands or by the transition of a TTL input/output through the digital I/O port of the acquisition system.

Raw Data (.nrd) files have a timestamp per sample per channel.  By default, Cheetah and Pegasus do not record this file structure and it must be manually enabled from the Recording Options window in the acquisition software.  The NRD file is a large data set that requires a separate hard drive to record the data to.  These files can be replayed through the acquisition software and many settings can be altered to achieve the desired output.

Video Tracking (.nvt) files are primarily used for X and Y coordinate tracking of the subjects head position and orientation.  Additional information is contained in the video file structure that can be used for additional tracking and analysis.

Take a look at the Data File Formats document for more information as well as your Reference Guide found from the File > Help menu in the acquisition software.  As always, contact support@neuralynx.com for further information.