Although similar, spelt has more protein and less starch than wheat flour.
http://en.wikipedia.org/wiki/Wheat#Nutrition
http://en.wikipedia.org/wiki/Spelt#Nutrition
This means that it will create a great structure but won't absorb as much liquid. This would result in exactly what you saw- it was sticky from water and protein and too loose to hold its shape but baked with a good crust.
The recipes I have seen use a mixture of flours that includes spelt.
Try adding less water.
Atta has a high gluten content, it doesn't sound like you need to do any extra work on gluten development. From your description of your method and your picture of your result I think you are under-kneading and under-proofing. Also, it sounds like you are knocking out what rise you do have. You should have a very elastic and smooth dough after kneading. If your gluten is not developed enough it won't have the elasticity you need or be able to trap the air needed for expansion.
You are adding sugar, oil and sometimes eggs and into your dough, all that is going to slow down the action of the yeast. Enriched dough takes significantly longer to proof (rise), 45 minutes for an enriched dough typically isn't enough. In any case you should be working to a result, not a time. A high hydration dough like yours should at least triple in size, if not quadruple before you move onto the next step.
You say you sometimes bake right after a first rise, you can do this if you proof it in the container you want but you have to make sure you don't lose any air. If you do a first rise and then move it to a tin you need to do a second rise to get the air back in it.
If you want a really airy dough don't knock it back, you lose all that hard work the yeast has done. Treat it as gently as you can when moving it to your tin or baking sheet and handle it as little as possible. Then let it rise again until it's the right size, then bake.
Something else that might be happening is that the crust may be hardening before you get full oven spring. In high hydration dough you get a lot of oven spring from the vaporization of water in the dough, the expansion of the air trapped in it and the yeast going crazy before dying. If your crust forms too quickly then the bread can't expand and it all gets trapped. Try putting a tray of hot water in the oven about 10 minutes before you bake the bread, it will create a moist environment that will keep the crust from hardening completely. Once the bread has sprung (about 20 minutes) you can remove the tray of water and let the crust harden up. Also, don't forget to score the dough on top with a sharp knife, that will allow expansion as well.
Best Answer
From the comments - you used a different brand of whole wheat flour this time around. My best guess (and really that's all anyone can do with something like this as there are way too many factors) is that this new brand is the reason for the difference in the bread.
Just because they are the same type of flour, it doesn't mean they are all milled, sieved etc. the same way.
It may be this new flour is:
All these factors can effect how the bread cooks as well as how much liquid the flour absorbs.
I would say it is very unlikely that your bread machine has broken since it sounds like the bread still cooked!
It's also unlikely that the bread will cause you any harm. An enriched plain loaf bread mix can be eaten raw (not that you'd want to).
Please feel free to edit my list with any other changes flour can have between brands.