@GrumpyOldMan
I'd love another pair of eyes on this one. I'll e-mail the
basepose and walk anim from my game directory tonight.

@Bwian
Thanks, that was a very detailed examination of the problem.
I've converted the stock walk anim and the converted anim
to text and here's the bone_pelvis anim blocks side by side:


Code:
0 bone_pelvis  animation data and deltas        0 bone_pelvis  animation data and deltas  
+0.0000122126 +0.9590483308 -0.0000000000       +0.0000084836 +0.6137909293 -0.0000000000 
+0.0017991858 +0.9512157440 +0.0901285559       +0.0012498223 +0.6087780595 +0.0626087040 
+0.0026300352 +0.9396055937 +0.1802604198       +0.0018269803 +0.6013475657 +0.1252197027 
+0.0000594494 +0.9203369617 +0.2704085112       +0.0000412971 +0.5890156627 +0.1878419816 
-0.0063111591 +0.9033862948 +0.3605716527       -0.0043841098 +0.5781672001 +0.2504746914 
-0.0137326801 +0.9005295038 +0.4507446289       -0.0095395437 +0.5763388872 +0.3131142557 
-0.0189423133 +0.9042277336 +0.5409182310       -0.0131584676 +0.5787057281 +0.3757542670 
-0.0211101491 +0.9193583131 +0.6310883760       -0.0146643762 +0.5883893371 +0.4383918643 
-0.0210416745 +0.9396334291 +0.7212522626       -0.0146168098 +0.6013653874 +0.5010250807 
-0.0201377589 +0.9517263174 +0.8114059567       -0.0139888953 +0.6091048717 +0.5636512637 
-0.0226440672 +0.9510992169 +0.9015470743       -0.0157299284 +0.6087034941 +0.6262686849 
-0.0249393098 +0.9356126189 +0.9916793704       -0.0173243415 +0.5987920761 +0.6888799667 
-0.0272242893 +0.9162625670 +1.0818185806       -0.0189116243 +0.5864080191 +0.7514960766 
-0.0254939552 +0.8969492912 +1.1719760895       -0.0177096315 +0.5740475655 +0.8141248822 
-0.0179745089 +0.8883986473 +1.2621510029       -0.0124861719 +0.5685751438 +0.8767657876 
-0.0077288523 +0.8950952291 +1.3523342609       -0.0053689247 +0.5728609562 +0.9394125342 
-0.0011719284 +0.9107339382 +1.4425106049       -0.0008140918 +0.5828697085 +1.0020544529 
+0.0010084946 +0.9343801737 +1.5326695442       +0.0007005609 +0.5980033278 +1.0646842718 
+0.0000120707 +0.9590483308 +1.6228270531       +0.0000083850 +0.6137909293 +1.1273130178
and the stock and new skeleton pose block side by side:

Code:
0    skeleton pose data, all bones including Scene_Root   0    skeleton pose data, all bones including Scene_Root   
+0.0000000000 +0.0000000000 +0.0000000000                 +0.0000000000 +0.0000000000 +0.0000000000                 
+0.0000000000 +0.0000000000 +0.0000000000                 +0.0000000000 +0.0000000000 +0.0000000000                 
+0.0952388048 +0.0007522844 -0.0000000837                 +0.0952389985 +0.0007520000 +0.0000000000                 
+0.0225614067 -0.4644486308 +0.0143960081                 +0.0225610007 -0.3418302238 +0.0143959997                 
+0.0241625141 -0.3995063901 -0.0316344053                 +0.0241630003 -0.2538871169 -0.0316339992                 
-0.0000000065 +0.2124619335 +0.0000000110                 +0.0000000000 +0.2124619931 +0.0000000000                 
-0.0002945312 +0.2115576267 +0.0000000300                 -0.0002950000 +0.2115579993 +0.0000000000                 
-0.0000617070 +0.2349729538 +0.0000000693                 -0.0000620000 +0.2349729985 +0.0000000000                 
+0.0003562541 +0.0108104832 -0.0034470418                 +0.0003560000 +0.0108099999 -0.0034469999                 
+0.0016836945 +0.1178485677 -0.0744605809                 +0.0016840000 +0.1178480014 -0.0744609982                 
+0.0132546537 +0.1300112009 -0.0273842514                 +0.0132550001 +0.1300110072 -0.0273839999                 
+0.1653587520 -0.0517836586 +0.0034831662                 +0.1762007326 -0.0517840013 +0.0034830000                 
+0.3022065163 +0.0111386608 -0.0137688387                 +0.3022060096 +0.0111389998 -0.0137689998                 
+0.2838369310 -0.0030556275 +0.0263377447                 +0.2853106558 -0.0030560000 +0.0263379999                 
-0.0102220690 +0.1300112009 -0.0273842178                 -0.0102220001 +0.1300110072 -0.0273839999                 
-0.1678021550 -0.0517837554 +0.0034834931                 -0.1762007326 -0.0517840013 +0.0034830000                 
-0.3021733165 +0.0111956345 -0.0144309197                 -0.3021729887 +0.0111950003 -0.0144309998                 
-0.2838011682 -0.0031999985 +0.0267028809                 -0.2853106558 -0.0031999999 +0.0267040003                 
-0.0952387750 +0.0007523637 +0.0000000981                 -0.0952389985 +0.0007520000 +0.0000000000                 
-0.0216095932 -0.4641435742 +0.0230794586                 -0.0216090009 -0.3414067626 +0.0230780002                 
-0.0250772368 -0.3986372054 -0.0406128988                 -0.0250770003 -0.2543957829 -0.0406120010
And that's all we're trying to do. Shorten the legs and scale the anims
to match. From your experiments the game is doing something very odd
with the new leg data and frankly I'm stumped as to what it is.

I've checked the quat data and of course it's exactly the same so nothing
going on there.