I don't think Filezilla has a setting to specifically ignore contents of a folder (at least I can't find one) and using Filezilla with default settings should work fine. There should be no need to delve into the settings to change things before upload Juicebox gallery files.
I guess if you wanted to troubleshoot your Filezilla methodology, you could check the transfer window (at the bottom) to make sure that the contents of the 'jbcore' folder are in the 'Queued files' tab, i.e. have been scheduled to be transferred to your web server (each individual file should be listed), and then switch to the 'Failed transfers' tab (after uploading) to see if (and why) any files have not been uploaded succesfully.
If the files are not even listed in the 'Quesed files' tab, then the contents of the 'jbcore' folder could be hidden in your Mac's file system and they simply have not been added to the queue (and Filezilla knows nothing about them).
In any case, I'm glad you have a workaround (and there are certainly other FTP programs out there, although I use Filezilla myself).