The rapid serial visual presentation (RSVP) paradigm is a method that can be used to extend the P300 based brain computer interface (BCI) approach to enable high throughput target image recognition applications. The method requires high temporal resolution and hence, generating reliable and accurate stimulus triggers is critical for high performance execution. The traditional RSVP paradigm is normally deployed on two computers where software triggers generated at runtime by the image presentation software on a presentation computer are acquired along with the raw electroencephalography (EEG) signals by a dedicated data acquisition system connected to a second computer. It is often assumed that the stimulus pre- sentation timing as acquired via events arising in the stimulus presentation code is an accurate reflection of the physical stimulus presentation. This is not necessarily the case due to various and variable latencies that may arise in the overall system. This paper describes a study to investigate in a representative RSVP implementation whether or not software-derived stimulus timing can be considered an accurate reflection of the physical stimuli timing. To investigate this, we designed a simple circuit consisting of a light diode resistor comparator circuit (LDRCC) for recording the physical presentation of stimuli and which in turn generates what we refer to as hardware triggered events. These hardware-triggered events constitute a measure of ground truth and are captured along with the corresponding stimulus presentation command timing events for comparison. Our experimental results show that using software-derived timing only may introduce uncertainty as to the true presentation times of the stimuli and this uncertainty itself is highly variable at least in the representative implementation described here. For BCI protocols such as those utilizing RSVP, the uncertainly introduced will cause impairment of performance and we recommend the use of additional circuitry to capture the physical presentation of stimuli and that these hardware-derived triggers should instead constitute the event markers to be used for subsequent analysis of the EEG.