Sepia toning, after bleaching to completion, tends to lose density in the darkest areas - so you will see some loss of contrast.

Were you agitating while the print was in the bleach? I usually rock the tray gently but continually while bleaching and have not had any problems with uneven activity even with 8x10 prints in 8x10 trays.

The bleach should effect the highlights first, but I find the standard bleach supplied with toners to be too strong - it is simply too fast to reliably pull the print out at the right moment because the bleach activity continues until washed off.