Hi,
The same bug that led to genes with incorrect ensembl identifiers like "ENSG00000000003 /// OTTHUMG00000022002" also introduced problems with symbols.
For example, the probe "11715138_s_at" would have been called "CGB /// CGB1 /// CGB2 /// CGB5 /// CGB7 /// CGB8."
This has since been fixed (on Sep 9) when we fixed the ensembl name issue. For example, the probe above would have a separate entry for each of the genes CGB, CGB1, etc.
If you are using symbols, you should have re-run your model after Sep 9.
Brian