SKB StageFive Pedalboard.....

I ran my bass through my pedalboard (which is powered) and found a noticeable difference in the tone vs. plugged straight in or even just through my tuner. Does something like that really affect the tone that much?? I use a Ric 4003 to a Walkabout Scout and it just sounded so farty through the pedalboard and so not farty through just my tu-2 and fuzz. Is there a better way to run effects out there without losing so much good tone?