[bitconductor]

I'm noticing approximately a 980 sample lag in the stereo files I'm recording in a session. I've got delay compensation on, and I'm not seeing any numbers in red in the delay compensation panels under the tracks in the mix window.
Hardware buffer size is set to the max, 1024 samples.
I've trashed the prefs.
The files are bus stems from a mix. 48k, 24-bit.
If I record a stereo file in a new session with no plug-ins, recording a track from audio playing on another track (either directly from a send or via a bus) there's no latency at all.
Has anyone got any ideas about this? It's a pain as I'm having to trim the files before delivering them.
Thanks.
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MacBook Pro (Retina, 15-inch, Mid 2015)
Processor 2.8 Ghz Intel Core i7
Memory 16 GB 1600 MHz DDR3
Graphics Intel Iris Pro 1536 MB
Mac OS Sierra 10.12.2
Pro Tools 12.7.1
Blackmagic Ultrastudio Mini Monitor (Thunderbolt 2)
Avid Artist Mix (Thunderbolt 2 > Ethernet cable)
Nugen Loudness
iZotope RX6