Rye Loaf

Did you use a formula/recipe specifically for rye+wholemeal?

Both rye and whole meal ferment faster/more than white flour, therefore they require less yeast or starter/levain.

(I have not been successfull using sourdough in my bread machine. The rise timings never seem to work right for me.)

So they (rye and whole meal doughs) tend to over-proof or over-rise, and the poor gluten of rye does not give enough scafdolding/framework to maintain air pockets that are produced.

in your pic... The air holes on the outer crust, against the pan, lead me to believe that your loaf had over-proofed. And the ragged top edges might be due to a too wet dough.

(If your dough is too wet/soft, the paddle tends to spin underneath it, with the dough mass sitting on top, tented, as a blanket, and the paddle bangs it around,  -- as opposed to maintaining a ball shape that gets "walked" around the pan.  At least that's what happens in my machine.) 

I've used my bread machine with whole meal too.  Whole meal needs the longer rise time of the "whole meal (whole wheat) program" setting to soften the wheat, and it needs the longer bake time of the whole meal program too.

So, to compensate for the faster rise, and excess rise of whole meal, but over a longer period of time due to the program, the yeast needs to be cut back compared to a white flour loaf.

My bread machine is also picky/sensitive to the hydration of the dough ball.  So I end up baby-sitting the darn thing, adding  water, adding flour, pinching off a little excess dough, so as to get the perfect size dough ball, at the right hydration/softness, so that the paddle "walks" the dough-ball around the pan correctly.  Does that seem familiar with your machine?

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Things to try:

- Reduce yeast or starter/levain by 25% to 33%.

- If you have some, try using maybe 10% strong white bread flour (12% or higher protein), to compensate for the rye's poor gluten, then use 30% rye, and 60% whole meal, to get your 1:2 taste ratio.

- Keep track of how much flour/water you add, or how much dough you pinch off, so in future bakes you can get the proportions right at the start.

- Because whole meal hydrates slower than white flour, the behavior during the initial mix "looks" off, even when it's the right proportion. So have faith it will work out, after you get the proportions "dialed in".

- To verify the mixing behavior when using mostly whole meal, I restart my bread machine after about 10 minutes into the initial mix.   So, by the end of the mix (after the restart) I can see that the dough has absorbed the water and will perform correctly during the knead cycle.

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 I realize all brands of bread machines are different, but maybe the above will explain some general concepts to help you get the most out of your machine and your ingredients.