There's a couple of problems with this release (and V2.07.11) we'll post a fix in few hours:
1. If you use -oSync with Illumina 1.8 fastq format files then the filtering of reads with llumina Quality indicator set will break the code that synchronously reports reads and output will stop at the first filtered read.
2. The new option to check read headers is --hdrhd not -hdrhd, some of the documentation is wrong.