I get this with a fastq file that worked just fine with 1.31.2:
mothur > fastq.info(fastq=IonXpress_001.Project_1000_400bp_2014-02-18.fastq, qfile=F)
10000
20000
30000
40000
50000
60000
70000
80000
90000
100000
100001
Output File Names:
IonXpress_001.Project_1000_400bp_2014-02-18.fasta
[WARNING]: your sequence names contained ‘:’. I changed them to ‘_’ to avoid problems in your downstream analysis.
There is supposed to be ~3.5 million reads, but the output fasta file contains only 100,000.