FASTA validator tool is a useful too for checking your custom FASTA file. If you have been splicing things together, such as adding newly sequenced genes to your database, or if you are searching against next gen sequencing data, it isn't uncommon to see a few (or a few thousand) errors when you import that new database into Proteome Discoverer.
If you see these errors, pull the File back out and run it through this tool. It will help you pinpoint the problems. Then correct them and put them back in. The tool can also help you deal with redundancy!