Freezing sauces?? Ew

The sauce sounds wonderful, and I imagine its flavors were very good when you firs prepared it. The problem you ran into when you froze the leftovers was that it's basically an uncooked sauce. The peppers are grilled, but the rest of the ingredients are added raw. Yes, they're puréed, but their cells are still in a raw state. Try tossing a raw onion in the freezer for any amount of time. When you thaw it, it's going to have that same unpleasant spongy (eew!) texture you described. The next time you make the sauce, try transferring it from the blender to a saucepan. Heat it gently just to a boil. Heating will break down and soften the cell walls that turned spongy on you. Then you shouldn't have any trouble freezing, thawing, and enjoying it.

Glass jar, good. 3 months no problem.

When you blended the oil with the rest of the ingredients (essentially water), you created an emulsion. Emulsions are fragile; they all have their breaking points. This one couldn't stand the freezing.

I made Bobby Flay's smoked red pepper sauce, which came out excellent, but again, after being in the freezer, then defrosted, the texture was all wrong. Using a glass jar to store the sauce was the problem? Or maybe being in the freezer for 3 months too long?

Recipe:
http://www.foodnetwork.com/recipes/bobby-flay/smoked-red-pepper-sauce-recipe/index.html

What was the recipe or what did you want to achieve? Red peppers have a lot of liquid and that needs to be taken into account. Sometimes they need to be roasted first.

When I defrosted the sauce, why did the consistency end up being a spongy texture...rather then a sauce, like it was when I first made it.

And what is your question?