Are you saying you made a stack of boxes as one model and imported it as a single entity? Or are you stacking lots of one entity within Game Guru to make the stack?
What does the collisionmode in the fpe say? Here are what the collision modes are (courtesy of T-Bone):
0 = box shape (default)
1 = polygon shape
2 = sphere
3 = cylinder
9 = convex hull reduction shape
11 = no physics
12 = no physics but can still be detected with IntersectAll command
21 = player repel feature (for characters and other beasts/zombies)
40 = collision boxes (defined in Import Model feature)
41-49 = reserved (collision polylist, sphere list, cylinder list)
50 = generate obstacle and cylinder from 1/64th up from base of model
51 = generate obstacle and cylinder from 1/32th down from base of model
52 = generate obstacle and cylinder from 8/16th up from base of model
53 = generate obstacle and cylinder from 7/16th up from base of model
54 = generate obstacle and cylinder from 6/16th up from base of model
55 = generate obstacle and cylinder from 5/16th up from base of model
56 = generate obstacle and cylinder from 4/16th up from base of model
57 = generate obstacle and cylinder from 3/16th up from base of model
58 = generate obstacle and cylinder from 2/16th up from base of model
59 = generate obstacle and cylinder from 1/16th up from base of model
1000-2000 = only one limb has collision Box Shape (1000=limb zero,1001=limb one,etc)
2000-3000 = only one limb has collision Polygons Shape (2000=limb zero,2001=limb one,etc)
AE