(Assuming single-line FASTA, as input.)

You could verify your sequences are of different length, as a way to troubleshoot:

$ awk '($0 !~ /^>/) { print length($0); }' in.fa | sort -n | uniq

If you get multiple values back, then you might investigate your input and cut them to the shortest length.

The following cuts the prefix of any input sequence string down to the shortest length:

$ SHORTEST_LENGTH=`awk '($0 !~ /^>/) { print length($0); }' in.fa | sort -n | uniq | head -1`
$ awk -vSL=${SHORTEST_LENGTH} '($0 !~ /^>/) { print($0, 1, SL); } ($0 ~ /^>/) { print $0 }' in.fa > out.fa

You could write different logic, if you wanted to trim flanking regions. It's a little more work to deal with an odd-numbered shortest length, however.