Dak reported the following bug on the mailing list:

I have a FASTA file that contain one sequence. I initialized FASTA reader as described in the tutorial, called process() and get one record as expected. However, if I re-initialized another FASTA reader opening the same one-record file, called process(1) and null is returned. If I tried to read two-record FASTA file, the first process(1) works, but not the second call to process(1) return null. Based on a superficial glance, it looks like the if statement at line 194 of FastaReader.java may be the culprit.

@andreasprlic created a branch, https://github.com/biojava/biojava/tree/DakFastaHeader which contains the failing TestFASTAReader.