Exactly which 060 Library did you copy over?
See here for different versions & the Latest:
http://phase5.a1k.org/index.html - Not sure if A3660's have their own Version?
Different versions of 060 Library can have different effects on different hardware combinations & that's before you even include the recent A3660 card.
Also, you state everything was okay for putting the original A3640 back in. Did you also replace the 040 Libs because they work differently to the 060 Libs.