Actually, I ended up using the latest 2.5.0.3041 BETA, so even that didn't help.
I am using this USB controller card http://www.amazon.com/gp/product/B00FPIMJEW/ref=oh_aui_detailpage_o04_s00?ie=UTF8&psc=1 which has FL1100 chipset, if that is what you meant to ask.
As for the MB, it is an off the shelf Dell XPS Studio 8100 for what it is worth.
As for the disks being advanced format (4K sector size), I think I have read somewhere not too long ago that external USB HDDs in particular, do some kind of sector size trick to maintain wider compatibility which would probably explain why Windows didn't complain about the larger disk size despite being mounted as MBR. Anyway, not too sure about this topic. All I can say is, they are the off the shelf, WD My Book external USB 3.0 HDDs connected to my Windows 7 pc via usb 3.0 hubs...One of them 3 TB and other 2 were 4 TBs.
-Hiranmoy
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