Genes that exist in old Affymetrix platform but not in the newer one
aI used to work at Affymetrix when most of these arrays were designed.  I was not on the design team itself, but I can maybe talk about this a bit more. 

RNA Array designs were built to cover anything that might possibly be real transcript in the mix of EST collections, cDNA, in silico gene detections and miscellaneous entries in public databases.  There were a lot of different people trying to find genes as quickly as possible and a good deal of it was not real gene naturally. I'm sure there was a reasonable amount of contamination in the millions of transcripts we took in as well.   

The team would find a good number of errors in the sequence database.  There is no way to submit this in a meaningful way to most bioinformatics databases by the way.  Just a note:)

When a new design came out the team would do auditing to see if any of the transcripts had fallen out of favor with the evidence and some of those 'genes' would be pared from the content.  

This is useful because DNA hybridization tech is very high throughput for the dollar but it has a background noise and even a probeset with no correspondence in the RNA sample will give numbers that are non-zero.  

RNAseq has similar issues from assemblies and sensitivity from limits of reads on the sample BTW.  There's no perfect solution as of yet.

BTW sometimes genes get renamed. I didn't get into your methods to see if this is a case, but something to keep in mind.