Also OS3.9 (and all pre os4 os's) only support up to 2gig partitions, programs dont like partitons above that size. Think about dropping it to 2 gig.
OS 2.0 and above handle >2GB partitions just fine (they might have limits at 4GB however). Workbench, HDToolBox and Info command might show funny values for (free) storage though, but those can be safely ignored. You probably also want to use QUICK-option when formatting the partitions. AmigaOS 3.9 most definitely supports >2GB.
Some applications (such as installers) have problems with partitions having more than 2GB free, though. They are equally broken under any AmigaOS version, including 4.