sequencing ssDNA PCR

[Marion D. Emerson]

Hello,

In our lab we routinely sequence ssDNA PCR products from 
mitochondrial DNA using the PCR primers in the sequencing
reactions.  This has worked well for us.
At this time I am trying to sequence ssDNA PCR products 
generated from RT-PCR of mRNA. Although I get great looking bands 
in both the RT-PCR reaction and the ss PCR reaction, when
I sequence (using the PCR primers), I get varying results.
One of the primers (5' to 3') works okay but the one in the 
other direction doesn't.  I get shadowy bands with lots of
backround, almost like a stuttering effect.  
Has anyone else had this problem and (hopefully) found a 
solution? 

Thanks in advance,    Marion

P.S.  we use a Taq sequencing method