The annotation packages for the Gene and Exon ST arrays in the current Bioconductor release (versions 8.3.0) are based on the na34 annotation files distributed by Affymetrix. It appears that there were some problems with their annotation pipeline. We asked Affy about the mouse Exon 1.0 ST arrays, and the response was:

"There was a large issue with the pipeline used for NA34, which is why the annotation numbers are so low.  It had significant issues and Affymetrix was well aware of them.  We took a great deal of time and generated a new pipeline for NA35 that we hope will resolve a great many issues people were experiencing with NA34."

The na35 data were released 15 April, which was after we released BioC 3.1. They have since (as of 1 June) released na35.1 versions for some arrays, which hopefully will be the last release from them. I am currently re-building all of the annotation packages for these arrays, and will hopefully have them available for download by the end of this week/early next week.

Edit: Please note that the new versions will be 8.3.1