Mutation during transformation/maxiprep - (Sep/07/2009 )

I have some DNA stock, a HA-protein in the lab left behind by some seniors. I transformed it and then maxipreped it. Now I see two minor mutations in the protein. Should I ask to repeat the sequencing, is a mistake in sequencing common (the peaks in the chromatogram clearly clearly shows the nucleotide mutation though). Should I pick up another colony and maxi-prep from that? My understanding is that theoritically all the colonies should have exactly the same DNA sequence (as it was made from a DNA stock). Please help.

pick another colony
do a miniprep
sequence
if it is correct then do a maxiprep

V