Have you tried a compressor/limiter before the envelope? This would even out the signal and prevent sudden peaks.
I am a newbie so take my input with the correct amount of weight. I only have active basses and have gone with many of the suggestions here to combat the issues you are dealing with. I have my compressor and an EQ pedal before my MF 101. I have the EQ Pedal set to control the signal going into the MF101 only. By doing this I do not have to make any EQ changes to my basses when I engage the MF101.... great threat and lots of great suggestions.
I've tried with a compressor, but not as much as I should probably. To be honest I use the compressor almost exclusevely for slap and I don't want to mess with the settings. An EQ pedal on the other hand... that might be the way to go, although I would prefer not to buy another pedal and (more improtanly) not to add another pedal to the chain. I will do it if I have to, but I'm sure I can tune up the pre-amp to get what I need
There is no reason an envelope filter cannot work as intended with an active bass. My 3Leaf Wonderlove sounds awesome with my basses, all of which are active. That is what the sensitivity adjustment is for. Also, I have it at the front of my board right after my octaver. Also, pickup selection and EQ is important. As @Lonnybass pointed out above, EFs like mids.
The problem is not the srings or the pups high, the bass it's fine, it's only with the filter. My guess was (and eveybody seems to aim in that direction) it's something about the frecuencies the pre-amp is feeding the pedal