I've never used any BioPerl modules myself (so I cannot say anything about their performance in general), but half an hour for reading ~200MB sounds extremely long indeed.  That makes me wonder if the file is maybe not stored locally, i.e. you're doing I/O with some remote share...

Could you check if running something functionally similar, but without Bio::SeqIO — in its most simple case

while (<>) {
    print if /^>/;
}
[download]

(or  perl -ne "print if /^>/" Test.fasta  as a one-liner)  takes similarly long?