Visual-vestibular conflicts (VVCs) are a primary contributor to visually induced motion sickness (VIMS) in head-mounted displays (HMDs). However, virtual reality (VR) comfort studies often rely on exposing seated or standing users to experiences with high intensity visual motion (such as roller coasters). These drastic VVCs tend to induce pronounced VIMS symptoms that can be reliably detected across individuals using common survey measures. The conclusions from studies using these extreme motion-based conflicts may not accurately generalize to naturalistic use cases in VR where efforts are made to minimize, rather than maximize, VIMS symptoms. In this work, we show that a subthreshold visual-vestibular conflict can induce measurable discomfort during naturalistic, long duration use. We first present a psychophysical study, conducted outside of an HMD, to rigorously identify the perceptual thresholds for sinusoidal noise in render pose (i.e., jitter) resulting in erroneous 3D motion of rendered content. We next introduce subthreshold levels of jitter to a Meta Quest 3 VR HMD and demonstrate that this can induce visual discomfort in participants playing the commercially-available game Cubism across a three-session, repeated-measures study. Importantly, we did not identify statistically significant comfort differences between control and jitter conditions with traditional pre- and post-test comparison of Simulator Sickness Questionnaire (SSQ) scores. Significant differences were only identified using the Motion Illness Symptoms Classification (MISC) survey administered every 10 minutes across each 90 minute session. This highlights the benefits of incorporating time-resolved data points and suggests that lightweight, more frequent surveys may be important tools for measuring visual discomfort in more ecologically-valid scenarios.