Are you specifying qualify values correctly for cap3?
For fasta files, the quality values must be in a separate file of the type fileoffilenames.qual.
From the cap3 documentation: http://staden.sourceforge.net/manual/gap4_unix_88.html#SEC161
EDIT: actually that link seems a bit outdated but the documentation link on their man site is down. Luckily its been archived: http://web.archive.org/web/20100423111938/http://deepc2.psi.iastate.edu/aat/cap/capdoc.html