Hi,
as can be seen by the comments to http://code.google.com/p/fluxcapacitor/issues/detail?id=36, sometimes reads shorter than the desired read length can be observed in the output of the Flux Simulator. These reads stem from cDNA fragments that are shorter than the read length. In reality, adjacent ligation and sequencing adaptors are sequenced in such cases. These sequences are highly variable between the different protocols, e.g. see a corresponding thread in the SEQanswers forum. Therefore, the current program outputs truncated reads, which would represent the read sequence after successful trimming of adaptor sequence parts.