In EMBOSS 6.6.0, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.

echo -e '>A\nAAAAAA' > test-1.fa
cat test-1.fa 
# >A
# AAAAAA
seqret test-1.fa:A stdout
# Read and write (return) sequences
# >A
# AAAAAA
mkdir test
seqret test-1.fa:A stdout
# Read and write (return) sequences
# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
# Error: Unable to read sequence 'test-1.fa:A'
# Died: seqret terminated: Bad value for '-sequence' and no prompt

See also http://lists.open-bio.org/pipermail/emboss/2014-June/008983.html

Done with the following workaround: the directory references/V was renamed references/V-C in 125524131bd57c084ee39374054b73784e6ae929.