I am having a problem with a project wherein I am attempting to use bones, and IK rigging on a shape that then needs to be instanced multiple times.  To recreate the problem simply, all you have to do is create a set up with some bones, and IK rigging.  Then create a model to place over the bones as skin and apply the skin modifier.  Now instance the model.  I recommend moving the instances around the scene in various directions to better be able to see the problem.  Save the file.  Reopen the saved file.  All the instances will be scattered into the scene.  Their scatter pattern is affected by the movements you have made with the instances from the original’s position.  In my case, my model with the skin modifier is made up of a couple of pieces, and they often break apart from each other as well as from their original starting position, regardless of being grouped, ungrouped, attached, or anything.  I’ve tried everything I can think of to fix this problem, and I’m still stuck with essentially an unsavable file.  I can delete the bones and IK rigging from the instances and the problem still occurs.  I have reduced the modifier stack to only include the skin modifier, and still no luck.  Has anyone else encountered this?  Is there a fix?  I am including a couple pictures below of one of my files in the working file, and then the saved file opened minutes later.  As you can see, the pieces (ie, the instanced creations from the boned and rigged piece) have gone flying off of the pink capsule, but the blue and green spheres and capsules remain unchanged.

Hmmm, it doesn’t look like my images are attaching. 
I also have them posted here, where I describe the specific situation a little more…
http://anatomyandart.com/blog/?p=130

I could be misunderstanding your problem, but must they be instanced? I think the problem is moving the skinned mesh away from the bones, to do this, make the copies References, not instances, then add an Xform and move them with that. The Xform will be above the reference line in the stack, so is unique to each copy, but everything below the reference line (skin and any other mods) will be instanced.

I have not used references.  I was told that using them would likely lead to more problems because I have so many and any one of them could potentially corrupt the parent as references.  But the motion works just fine in the instances without bones or rigging.  They follow the parent perfectly.  The problem doesn’t occur until I save and reopen the file.  Is there a way that things are supposed to go to make instancing and rigging work together correctly? 
I’m also having a little trouble understanding just what Xform is.  Apologies if that’s a dumb question, but what does that do?  Maybe it’s the missing piece to my puzzle.

The Xform is basically a Transform Modifier. It does exactlty what the transform tools do, move the position, change the orientation or scale, but in the form of a modifier in the stack.
You may ask why, because you can do all that with the tranform tool. But being a modifier, it can be treated like other modifiers. You can apply it to a sub-object selection or soft selection, move or animate it’s own centre independant of the object’s pivot, switch it off and on etc… lots of things you can do with it.
In this case, apply it to the whole mesh. The reason not to use the move tool for this is that will take the mesh away from the bones and stop the skin mod working. Because Xform is a mod, the skin mod below in the stack is still in the right position for the bones. If you used it on a instance, all copies would have the same Xform.
I don’t know why you are so frightened of references, think of it as an instance but with unique modifiers on top of it.
If you want to try it without fear of corruption, save a different version of the file first.