Niggo
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Niggo's post in Some drives show up as "has zero size" in JBOD was marked as the answerSooo, after all this time... an update.
At some point I realized I was using SAS and SATA disks in the same enclosure. Same exact disks except for the connector. Now, I did know that, I was just not fully aware of the implications. The SAS disks, obviously, showed up just fine when plugging in two controller into the disk shelf. You might already know where this is going. The SATA disks, however, were not. This is due to the fact that SAS disks are capable of connecting to two controllers/HBAs simultaneously but SATA disks are not. Thus, whenever I plugged in the second IOM on the disk shelf, the SATA disks kept randomly deciding which controller they were going to talk to. The SAS disks did not mind at all, since well, they are dual-controller capable.
Well, so much for that.