Marqs has added saving of the Advanced timing options together with profiles in firmware 0.75 so not being able to save is expected. The red light just comes on because its resyncing with the new timing options.
You should set H.samplerate not lower than 858 with the Dreamcast or else you will be losing detail so samplerate 906 should be good.
Did you try to cycle the input on the tv after changing H.active? Sometimes I have to do that on my Samsung monitor after changing H.active to make it stretch properly.