Baking – Undercooked cookies

It may be because of the type of yeast being used. Quick-cooking bread machines (1 hour cycle) typically requires "instant" yeast which rises much faster. Standard-cooking bread machines (2-3 hour cycle) need regular yeast, which is active longer. It sounds like you're using instant yeast in a standard recipe; thus the yeast stops working before the bread machine gets to the second rise cycle. Under-cooking may be because the resultant dough is denser than the machine expects, thus doesn't heat through in time.

Unfortunately the trade names for "Regular Active Dry" yeast and "Instant Dry" yeast can be very confusing.

This looks to me like the symptoms of too much flour - probably way too much.

Measuring baking ingredients by volume instead of weight is always a crapshoot, although it shouldn't be that far off - my guess is that either the flour was heavily compacted, or perhaps the baker's mind wandered off and she accidentally added an extra cup.

Overmixing (i.e. by using an electric mixer) is a common problem with cookies but the symptom of that is a hard and gritty cookie that doesn't rise - not one that rises too much and has unbaked flour in the center. As far as I know, that can only happen with a huge amount of flour. Obviously, too much flour would also result in a much denser dough.

What you ended up with seems to be more like a quickbread - almost a scone - and there is indeed not an awful lot of difference between the two aside from the ratios and the creaming of butter.

Excess flour probably wouldn't result in a stickier dough, but stickiness is more due to temperature than anything else. If you're finding the dough too sticky to mold then make sure it's thoroughly chilled - that will make it easier to work with.