Disks > 512 GB are officially not supported on eCS / ArcaOS. But unofficially, they work with some tricks. You need to use DFSee to create volumes on them, and assign drive letters. The reason is a non-standard geometry of such drives. DaniS506 and OS2AHCI on drives from 512 GB to 1 TB assign a geometry of 127 sectors per track, and for drives from 1 TB to 2 TB, a geometry of 255 sectors per track, instead of 63 standard sectors per track. Some tools like lvm.exe or IBM Boot manager, or AirBoot, may not like such drives. So, special tricks with DFSee are required. I'm using two 2 TB drives on two machines, successfully, but OS/2 Boot manager or AirBoot don't even boot a boot sector. I use my FreeLDR or _dixie_'s QSINIT instead, as they aren't so picky regarding the disk geometry.
PS: I observed JFS CHKDSK/FORMAT errors with such drives, too. Looks like in your case too.