I took another try at figuring this one out and here's what I've determined for 5.0.1.  The progress bar on the Story work item is what I've started calling a combined progress bar. Combined in that the "Estimated" percentage is actually an average of the Complexity and Time estimates.   So with one Story work item and child Task work items it worked like this:

Case one: Story complexity-unassigned, Task 1-no estimate, Task 2-no estimate --->> Progress Estimated % on Story-50%
Case two: Story complexity-unassigned, Task 1-no estimate, Task 2-estimated --->> Progress Estimated % on Story-67%
Case-three: Story complexity-unassigned, Task 1-estimated, Task 2-estimated --->> Progress Estimated % on Story-83%
Case four: Story complexity-NON-zero value, Task 1-estimated, Task 2-estimated --->> Progress Estimated % on Story-100%

Our initial working assumption was that the Story Progress Estimated percentage would be derived from the child work items.  So in Case one through four the expected %'s would be 0, 50, 100, 100.  The second possibility was that the system was considering the Story as part of the estimate group, so there are actually 3 work items to consider.  So in that case the expected %'s would be 0, 33, 67, 100.  But that's not how it works, either.  What did work was to consider each measure, complexity (Story Points) and Estimate (hours) separately, then average the two. So to get to the results in Case's one through four above it worked this way:

Case One (0 complexity, no task estimated)
Complexity Estimated=100%, tasks estimated 0/3-0%, average 50%

Case Two (0 complexity, one task estimated)
Complexity Estimated=100%, tasks estimated 1/3=33%, average 67%

Case Three (0 complexity, two tasks estimated)
Complexity Estimated=100%, tasks estimated 2/3=67%, average 83%

Case Four (non-zero complexity, two tasks estimated)
Complexity Estimated=100%, tasks estimated 3/3=100%, average 100%

I know this doesn't cover all the options, but I did additional tests with additional children and this calculation scaled up well.

AND you may have noticed the divisor in the fraction for the tasks estimated percentage.  In this example, you might expect it to be 2 since there are two tasks.  To get the numbers to work right you need the total number of work items in the parent/child configuration, so in this case it's 3, 1 story and 2 tasks. Now, why 1 Story without a complexity value shows a Progress Complexity of 100% is still a mystery only IBM can answer.

We checked multiple sources including jazz.net, help files, and even some IBM sources and no one had an answer.