Delay OVER compensation on input recording?

[PATofNAVAR]

Sorry for the strange question but we are seeing a strange issue.

My current setup is the following:

I have the following gear connected in my system:
APOLLO16
UAD-2-SATELLITE-TB-QUAD
APOLLO-TWIN-MKII-QUAD

Mac Pro (Late 2013)
3.5 Ghz 6-Core Intel Xeon E5
64 GB 1866 Mhz DDR3
Glyph 8TB

ProTools 12.7.1

We are experiencing something very strange. We all know about latency and issues with things being behind based on processing, DSP and other issues.

What's happening with my recording is that while recording through my silver Apollo 16 (thunderbolt) and into pro tools, my recordings are consistently 1000 samples EARLY. This isn't a fluke or being irrational or bull headed thinking the drummer is "perfect" because it's happening with drums, bass, guitar..etc.

It almost seems like it is Delay OVER compensation.

We tested this by opening console and then protools and heard a delay when recording a basic metronome. Now this delay makes more sense if we had some plugin on the session. We DO have plugins on the session, but the CPU never gets over 4% usage. We are at the lowest hardware buffer. I get the delay, but what I can't figure out is how the actual recording is 1000 samples early. We can and have been just shifting the whole ting over, but that seems ridiculous.

Anyone ever had this issue before that can help??

[lesbrunn]

Plugins on the master bus can do that. Maybe it's best not to put plugins on your mix buss till you're done with your recording.

[PATofNAVAR]

Actually there was no master buss, everything was just running straight to output 1-2.

[lesbrunn]

Do you make use of the Apollo's low latency by monitoring through the interface?