I just built up an 09 s-works epic to upgrade from my 05 epic.
I can feel the Brain open in the rear suspension on the 09 (no matter what setting) whereas with the 05 it was a smooth transition. Is this normal?
The difference is the way the "newer" brain works. The older brains were on a timer-type setting.... basically the valve opened and closed via a brass sleeve in a gel reservoir. The brain remained active while the hammer slowly sank through the gel (roughly 5 sec.). The newer brains operate on a sort of oil bath with a similar hammer covering the flow ports to the shock. Because it is oil instead of the gel it is a more instant change. This is more efficient, but also feels a little more "on/off" clunky.
I personally like feeling it come on and off... Thats how I know it works. Just set your pressure and rebound just right and the "clunk" feeling will become less noticeable as the shock is set how you like.
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