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The position of the bones on the arms changes when I switch modes and I cannot figure out how to fix it..

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The problem is created by the IK bone pivot not align to the child bones in edit mode. Use the cursor to snap all the bone pivot to the same location. Also make sure that your bones are rotated so that it is perpendicular to the front view as much as possible - at rest.

Attached is are the bones rotated and all the IK pivots of the bone aligned properly.

Snapping the bone pivot onto the same location do the following - In edit Mode.

  1. Select the end bone nub.
  2. Use CtrlS choose "cursor to selected"
  3. Select the other bones hit CtrlS choose " Selection to Cursor"

  4. If required , go to pose mode and reset all rotation and transformation using AltG and AltR

    enter image description here

Below, you can see 3 spherical nub aligned. The 2 red ones and the big green one needs to all be aligned in one spot using the "Cursor to selection" then " selection to cursor" method.

enter image description here

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  • $\begingroup$ sorry I don't get step 3. Which bones do you mean? When I selected Lower_Leg.L and selection to Cursor, the bone gets dislocated. BTW Alt G sometimes doesn't seem to work after I make a lot of changes and I have to resort to Ctrl Z. $\endgroup$ – A Allen Feb 14 '16 at 15:07
  • $\begingroup$ You have 3 bone at the foot that needs to be at the same xyz coordinate at it's pivots. Namely the lower leg, the foot and the IK foot bone. If you looked at my blend file I have also reposition the knee bone and the elbow bone and alter the "pole angle" of the constraint. You will also find that I have done the same to the lowerarm and the arm IK bone so that their pivot point is one the exact same spot. $\endgroup$ – hawkenfox Feb 14 '16 at 17:23
  • $\begingroup$ As long as all your bones are aligned properly in edit mode. Hitting Alt G and Alt R will work. As all the transformation will reference back to the edit mode's bone transformation coordinate. When your IK object location do not match your child bone's nub it can cause resetting the bone in Pose mode to not behave appropriately. $\endgroup$ – hawkenfox Feb 14 '16 at 17:25
  • $\begingroup$ You need to first do "CURSOR TO SELECTED" meaning you have to select the first target you want all bone to target to. Select the Lower leg bone nub, it's the spherical shaped object highlighted in light blue in the image. Then select the other bone nubs ... eg. the foot spherical shaped nub and the foot IK spherical shaped nub. and do "SELECTED TO CURSOR" $\endgroup$ – hawkenfox Feb 14 '16 at 17:30
  • $\begingroup$ Don't go selecting the whole bone you only need to align the bone nub, which are the spherical ends of the bone object. $\endgroup$ – hawkenfox Feb 14 '16 at 17:39
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The answer is sort of correct. Hawkenfox meant to say "Shift S", not "Ctrl S" while in edit mode on an IK bone. This should solve any confusion. Ctrl S is used to save the file. At least it is in Blender 2.78a.

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I just had the same problem, even by applying "with automatic weights" the armature would be out of the mesh, then I realized that I hadn't applied my mesh's modifiers, such as subdivision surface, I clicked on the apply button then I went to object mode and selected my character then shift selected my armature and ctr+p then "with automatic weights" that was it.

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