[GenoMax]

Following applies to MiSeq only (I do not know about the other platforms, please check)

The fastq files from the MiSeq do not contain the barcodes after demultiplexing by default. Actually you dont need this information for further analysis once the demultipelxing is done.
Having said that, if you really need these sequences for some reason you can force the system to provide you with that information by changing the MiSeqReportor.exe.config file in C:\Illumina\MiSeq Reporter.

Just add this tag to the appsettings

<add key="CreateFastqForIndexReads" value="1" />

and restart the service, and requeue you run for analysis.

Hope this helps with your issue.

This workaround will create a *separate* file for fastq sequences of tag reads. It will not create the type of fastq ID's that CASAVA or bcl2fastq produce.