Fix incorrectly skipped long breaks #443

[AdamPS]

Proposed resolution

For both problems in the issue #443 the fix is similar: move to code to handle reset of breaks to when a break ends rather than when it starts.

[slgobinath]

Hi, I am working on a major code refactoring because the code became more complex and hard to understand the flow. I am also fixing one issue you addressed in this PR (breaks shuffled before taking them). Please wait until I finish the refactoring so that we can avoid conflicts later.

[AdamPS]

That sounds great I look forward to it. I updated the description in the issue #443 to explain two situations more clearly.