No personal experience, but from other people's posts here, it seems the active EMGs are putting out too high a voltage(?) for the input circuit of the Spider amps.  Solution that seems to work for people is to use a stompbox (any kind, but should not have 100% bypass) between guitar and amp to temper the signal.

I had a spider 75 and I gave it to a friend as a traded for another guitar after I purchased a pod hd 500. I had actives in my guitar and they played great and tuned very accurately through the 75. And now my friend has that amp and is having tuning problems luckily playability Isnt affected tho. The key difference between our setup is he has an emg setup and I have blackouts. Out of every thread I've read here, emg seem to have a consistent problem with the spider series. However blackouts don't reflect the same issue. But the only fix I've came across was mentioned earlier and that's use a pedal that doesn't offer true bypass. Having used my 75 for a few years, I would recommend a noise suppressor and turn off the one built into the amp that way you can at least utilize the pedal in your signal chain effectively instead of having to lug around another piece of equipment just so you can play hassle free.