Why do I get doughy centers of my loaves?

Rye flour contains amylase, which breaks down gluten structure. Amylase is neutralised in an acidic environment, which is why rye bread is usually made using a sourdough starter.

You'll either need to switch to making sourdough bread or find an alternative to using rye for the health benefits your looking for.

are fermenting faster so cut back on some of your proofing times (or add less yeast) and get the dough sooner into the oven.  

You can also squeeze in a little lemon juice to up the acid as Jon mentioned.  

If you are adding over 40% rye flour to the dough, think seriously about starting a rye sourdough starter.  

Mmmm now that is interesting. I have had the same problem. I also don't like white bread but have troubles with whole flours. I use mixes of white and rye/whole meal/spelt. From time to time I get the doughy centres, and almost always very little, to no oven spring. My biggest problem however is getting proper gluten development. I've done all the different knead methods, but don't seem to get that smooth silky look. Its very frustrating.....When I do a white I have no problems and it always comes out perfect.

The family is not to fond of sourdough bread so that puts me in a difficult situation. I'll give the lemon juice a try. Thanks for that Mini Oven. When you say a little...Is a tsp per 500g flour about right?

I think that, for a 100% whole-grain bread, you've got some nice spring there. Unfortunately, unless you're willing to invest in a nice mixer and spend 20-30 minutes beating the hell out of the dough (cf. txfarmer's shreddably soft whole wheat bread formula and "technique"), its going to be tricky to get the kind of gluten development that's possible with white flours.

The problem lies mostly with the bran particles, which can never be milled as finely as the endosperm and germ, and which will always upset a high level of gluten development. Additionally, rye seems to resist gluten development to a certain extent, especially in such high numbers.

As far as a sourdough starter is concerned, switching to 100% rye is not a bad idea, but just be aware that it will ferment differently than a wheat starter, typically quite a bit faster. And rye absorbs water differently than does wheat, so a 100% hydration rye starter will have a much different texture than a 100% hydration wheat starter. You don't necessarily need to start from scratch, just start feeding your current starter exclusively with rye flour, and voilà, you'll have yourself a rye starter in no time. In theory, there will "always" be traces of wheat somewhere in the starter, but over time they become so minimal, and rye is a strong enough presence to quash any outside influence.

Good luck !