Since then, I've observed an odd behavior - bowtie2 will not list the new fastqsanger files in my history.

It will work with files that had already been groomed before the upgrade.

I also see that the groomer is not recognizing fastq files.

The format does seem to be correctly set for these datasets. Is there more than one place that a dataset's format is stored (and therefore get out of sync)?

Could I have messed up the data types xml file? 

It looks ok.

Seems unlikely that this would be a global problem since nobody else has reported it… but it does seem a bit subtle (only affecting newly tweaked files)

Any ideas?

Brad