I am working on a vector based on WoW's Xal'atath character.  Her eyes have an interesting radial gradient from blue to black and the iris is outlined in a very pale pinkish circle.  Yes, her eyes are not natural, she is a being of the Void.  Anyways I have two problems.  First, if I group the pinkish circle with the gradient of her iris, I lose the gradient completely.  I can't even fix it with undo, I have to remake the gradient completely.

And here's the worst part, if I close the document and reload it, I lose the gradient again.

How can I fix this issue?  I might be forced to find other software if there's no way around this bug, I need this gradient to replicate the effect her eyes have on her in-game model.

That's not something I've seen here. 

As usual, I'll suggest resetting the preferences as the first step.

I you have a sample Inkscape svg file to share that shows the behavior, that could be helpful.

Options could be to use a single gradient fill to make the iris, or use a gradient stroke.

Sounds like the behavior when you move an object and the gradient to transform with an object icon isn't toggled. http://tavmjong.free.fr/INKSCAPE/MANUAL/images/ICONS_PNG/status/transform-affect-gradient.png

http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Attributes-Fill-Stroke.html#Attributes-Gradients

And also, that your grouping has some serious transformations going on, that interfere with your image. 

I'd try ungrouping everything and regrouping after if necessary. 

Preferably everything copy/pasted to a new layer too, just to be sure. (Layers can also have transformations.)