Awesome, some with the same problem I had/still have.
Yeah EMG81, great sound, I have EMG81 active set on my guitar. I have recorded some DI's myself and realised that my DI are clipping. There has to be tons of threads about that. So when I was asking questions here back then, I got answers and started my science project.
I checked: (/replaced and it wasn't the problem)
1. wiring
2. potentiometers
3. pickups
4. output socket
Then you have nothing else left but your, let's say DI box or soundcard. That might be the problem right, because I checked my complete guitar except the wooden body right...
hehehe
.....yeah, but it wasn't the soundcard nor was it the DI box. Worked just fine with another guitar with EMG81.
so then I came up with my conclusion, that tight, heavy, massive wood can be one of the factors here. You see, I tried my EMG81 set on a Jackson flying V and the DI's weren't clipping. When I recorded with my guitar DI's were clipping. I was recording with the same gear and settings.
To sum tha fuck up once and for all, about this EMG81.
These pickups tend to clip, on some guitar less on some more. Wood and body structure( bolt on neck / neck thru body ) are only one of the factors. There is also distance between the strings and pickups.
So if it's clipping, check your devices and input levels, if that is OK, just accept that your guitar is clipping and make that 18V so the peaks of you DI signal will be cut far more less than on 9V.
Thank you and godspeed!