In 5.5, ScreenPassVS (ScreenPass.usf) only emitted stereo outputs under MOBILE_MULTI_VIEW && INSTANCED_STEREO, so desktop native ISR never affected its signature.
In 5.6 the signature was refactored to FStereoVSInput/FStereoVSOutput, whose contents are gated on plain INSTANCED_STERE, so with desktop native ISR enabled, the VS now outputs EyeIndex : VIEW_ID (and SV_ViewportArrayIndex) between TEXCOORD0 and SV_POSITION.
Most pixel shaders paired with ScreenPassVS were updated to declare in FStereoPSInput StereoInput (e.g. PostProcessTonemap.usf, CopyRectPS), but PostProcessVisualizeLevelInstance.usf MainPS was missed since it declares only TEXCOORD0 and SV_POSITION.
So SV_Position lands on mismatched registers between the stages.
Fix: Add in FStereoPSInput StereoInput, between UVAndScreenPos : TEXCOORD0 and SvPosition : SV_POSITION in MainPS of Engine/Shaders/Private/PostProcessVisualizeLevelInstance.usf, matching the pattern used by PostProcessTonemap.usf. Verified fixed locally on a 5.6-based engine.
[Attachment Removed]