The first explanation is that too much template has been added to the sequencing reaction. In this scenario the signal intensity decreases due to depletion of the fluorescently labeled ddNTP's. The second possibility is the presence of secondary structure. For G rich templates dGTP chemistry is helpful. Other cycling parameters can also be employed to get through repeats and hairpins.
Consultations are available.
Multiple products are seen as peaks within peaks. In such a sample the signal strength is good but more than one peak exists. If the multiple products begin after the multiple cloning sight for plasmid DNA more than likely there are two clones present. If the multiple products exist from the beginning of the sequence than two priming sites probably exist. For PCR products there is also the possibility of an insertion or deletion.