If you think presenting those pathways make sense for your study, you can relax the criteria.
1) You can use p-value instead of FDR/Benjamini
2) Even then if you don't get, you can also go upto p-value < 0.1 (10%)
3) Otherwise, you might be using very stringent criteria during differential expression analysis (might missing out important genes). Reduce the stringency and try pathway analysis with bigger list of genes. This might bring your important pathways to be significant.
If you are interested in batch analysis (simultaneously doing pathway analysis for multiple lists filtered with different criteria), try out GeneSCF.