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I didn't think input lag was ever an issue with multi GPU.
As a generalisation no, some configurations of SLI and VSync don't play nice tho.
I thought that this was the case with both multi GPU and single GPU with V-Sync, hence the popularity of triplebuffering and adaptive v-sync.
I am pretty sure that SLI cause an extra frame of input lag vs a single GPU...
I was wondering if this has been resolved recently.