This issue is not high on my priority list, it was just something that crops up every now and again, and I was hoping that someone else had experienced it, and possibly had a solution or an explanation as to why it happens.
If I could understand why it happens, I will try to avoid it while designing, probably something silly that I am doing with the workflow, esp considering that I had to modify the part a few times, and added cuts out of order.
We take much investigation on this behavior, and it is a known issue for us. When looking into the extrusion, you will find that the key factor is that the symmetric flip direction is used for extrusion cut. For this issue, the reason why is pretty simple. Edit the extrude feature and change extent from All to Distance, you will see the distance value is set to zero, which is illegitimate. As a result, the dialog does not like the condition and then greys out the OK button. To fix the issue, you could have two choices.
Choice A: When switching extents type from Distance to All, simply give a meaningful value like 1mm or 1in (default value), instead of zero.
Choice B: Do not check for Distance value when extents type is set to All.
Generally Choice A would be a better solution and easier to implement, since any value Inventor sets should be meaningful.