Since the carpet has previously only been cleaned by what is realistically a maintenance there was, in all probability high degree of impacted soil at pile-base.
You have cleaned by a deep-clean method but it sounds like the clean was less efficient than was required and that some of the soil not removed has wicked to the surface during drying.
Bonnet buffing with a bleaching agent will not solve the problem, what is required is a though extraction clean without missing out any of the steps : pre-vacuum, pre-spray, agitate well, extract with good flushing and leaving the carpet as dry as possible.
If you have only low-power equipment it may be worth post-bonneting to lessen the risk of further up-wicking.
There is a small chance that the dirty patches were partly protected from your bleaching and may be a slightly darker colour after cleaning.
John.