No difference if Trails is on or off.
I have dived in to the VST3 specs to get some insight into this. All audio processing plug-ins have to implement an interface called IAudioProcessor. In there is a method called getTailSamples that are supposed to return the number of samples that are needed to let the tail decay. The VST3-host can then use this information for whatever it wants. Cubase use it to reduce cpu load by asking the plug-in how long the tail is and then disables the plug-in if there's no audio input and the tail has decayed. This resource saving function can be disabled by unchecking a checkbox in preferences, hence why it works when I uncheck the setting...but at the cost of all plugins staying active, regardless if they are only used for a single bar in the beginning of the song. Reaper don't have this feature what I can see, all plug-ins stay active, that's why it works there.
I also downloaded Steinbergs TestVST-host. It contains some conformance tests and, surprise, it failed in the "Check tail processing" test. :-)
As this only applies to VST3, it fails in Cubase but works in Logic (AU plug-in version). All this makes me fairly sure this is a genuine bug, it would be really odd with a problem in my setup that only affects Native and not other plug-ins.
I submitted a ticket but I'm having a hard time getting past 1st line support, I've had to answer twice that unchecking the checkbox is not an acceptable solution.