Occasionally users on Windows may find that custom BLAST reports no hits, even when using a sequence contained in the BLAST database as the query. To fix this, try the following:
Reinstall the custom BLAST executable to a new location. To do this, go to Tools->Add/Remove Databases->Set up Search Services, and type in a new folder name for the location of custom BLAST (e.g. Users/Username/Geneious 7.1 Data/BLAST2). Click OK to let Geneious do the setup. Then try making your database again.
If option 1 doesn't fix the issue, you may need to install the 32-bit BLAST executables instead of the default 64-bit executables. To do this, delete your existing custom BLAST folder(s) from your Geneious Data folder, then manually download the win32 version of BLAST (ncbi-bast-2.2.29+-win32, available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/). Extract this file to your data folder. Then go into Set up Search Services and point Geneious to this location (which should be Users/Username/Geneious 7.1 Data/Blast). You will then need to remake your databases again.