Are you using static mount points (manually added by you to /etc/fstab) or are you allowing Ubuntu to dynamically mount them under /media?
If the latter, you’ll have a better time if you create/use static mount points as described in this how-to post:
But I agree with @Menel that it would be a good idea to move to a Linux-native filesystem such as EXT4, if possible. Or, if you’re going to be moving the drives between Windows and Linux systems, the exFAT filesystem might be a good compromise.