When you bypass DSP plug-ins in an automated mix, the actual change in state may sometimes occur slightly late. Setting the Audio preference for Sample Accurate Automation to "Volume, Pan, Sends, Plug-In Parameters" won't help.
For optimization reasons, bypassed plug-ins are removed from the CPU load, so it's not possible to change a plug-in's bypass state and have it be sample accurate. Instead, place the automation nodes for the plug-in's bypass and enabled states slightly earlier in your tracks.