Indeed, it only seems to happen in FL... but something tells me it's not necessarily all FL's "fault". Sometimes UVI engine based plugins play ahead of everything else, ignoring even the latency of all the other generators/effects - with 20ms latency setting UVI engine plays 20ms ahead of everything else
Sometimes they are just late compared to other instruments, but the amount of delay seems to be random... if you're lucky, it matches a note value nicely, the usual issue I've seen and heard of is that UVI engine plays exactly 16th note late =)
Hopefully we'll hear from FL insiders about this, I'd assume it's been discussed on FL forums and there's been an answer regarding this.
Regards,
JMH