The 25% adjustment and 40% account for different things. The shear wall and diaphragm table are based on principles of mechanics, see APA Research Reports 154 and 138. Basically a single fastener value, Z, is multiplied by load duration factor (1.6), diaphragm factor (1.1), number of nails per foot, and a few ~0.9 empirical terms sometimes apply.
The shear wall and diaphragm tables are calculated for wind or seismic (a short term load), which corresponds to a load duration factor of 1.6. If you need your shear wall to resist a long term load then a different load duration factor should apply. The 25% is from the pre-1991 NDS load duration factor which used to be 1.33. 1/1.33 = 0.75. Today if you want to adjust to a "normal" load with load duration factor of 1.0 then the adjustment would be 1/1.6 = 0.625. The codes need to be updated to reflect this. Look for a code change in the 04/05 ICC code development cycle. Also, what I describe is stated in Breyer et al. Design of Wood Structures 5th ed. I should note there is no evidence the "old" higher 0.75 adjustment is too high. The descrepency is a result of the new (in 1991) DOL factors (was 1.33, now 1.6) and diaphragm factors (was 1.3, now 1.1).
The 40% increase for wind has nothing to do with load duration. The 40% increase for wind is to lower the load factor due to historical good performance and since "we know wind loads so well".
One other thing. The framing species adjustment has changed too in the IBC. It's simpler in my opinion.