AIUI, the ticket price shown on My Flights is the price on the ticket. If you could get a printout of the e-ticket receipt itself (as opposed to merely an itinerary showing the ticket number) with the full breakdown into base fare plus all the different bits of TFC, that would show the same as what is shown on My Flights.
If your travel agent has charged you more than that, one possible explanation is that they've paid the lower price to the airline and kept the rest; and if you were to change the ticket, they would pay the change fee and fare difference to the airline without charging you any more, gambling that in the long run they will take more from customers who don't change than they pay to the airlines for customers who do change. Other explanations, of course, are also possible.
One interesting thing about seeing the My Flights ticket price breakdown is the total on tickets where you've only paid BA the RFS cap. The total TFC written on such tickets can be rather more than the RFS amount paid.