GeneSpring uses a so-called “column mark” for annotations during custom technology creation. If column marks were inappropriately assigned at that time then you may encounter this issue. Please refer to section 3.2.2 Update Technology Annotations in the GeneSpring user manual for more information.
If the column marks were selected correctly and your pathway analysis still results in no matching pathways, please contact GeneSpring support at informatics_support [at] agilent [dot] com for assistance.