External Hard Drive (USB3.0) only works through USB2.0 hub

For quite a while now some of my external hard drives have not worked when directly plugged into my Macbook Pro (Mid 2012 running 10.8.5). They work perfectly when plugged into a USB hub and then into the macbook but not directly to the mac. Standard small USB flash drives work fine straight in to the macbook, the real problem appears to be USB 3.0 hard drives. These will not show up on desktop or disk utility unless I plug them in via a USB hub (which is USB2.0). The hard drive format doesn't seem to be important, currently my Mac OS Extended Time Machine backup HD is only working through USB hub, and my MyPassport WD external drive is NTFS and hasn't worked directly into the Mac for a while now.
Normally this is not a big issue, but when I am on the go it is useless to carry a USB hub around along with a MyPassport hard drive! In addition, there are times, such as when backing up, that I want the speeds offered by USB3.0 from my macbook to my hard drive.
What could be the problem? I run NTFS for Mac OSX, not sure if that would cause an issue with the direct connection.
Please help, this one is grinding my gears!
Thanks

WD Black 2TB back in summer sold for about $179 and excellent choice.
Very important as to what controller you get and what it supports, besides Mac Pro 2010, 64-bit mode drivers.
With 4 drives you may or may not want a card+case that is Port Multiplier.
To use 4 drives you may want 4-port SATA.
The ideal might be two PCIe cards and two cases, so your data and backup are not on same controller and case. Or not.
avoid Port Multiplication
(Positive) Reports from OS X users of eSATA PCIe cards with Port Multipler cases
Sonnet Tempo SATA 6Gb 2-Port PCI Express
NewerTech MAXPower eSATA 6G
http://eshop.macsales.com/search/pcie+Serial+ATA
WD Black 1.5TB $169 / 2TB $249
http://www.amazon.com/Western-Digital-Caviar-Internal-Desktop/dp/B004CSIG1G/ref= sr_1_12?s=electronics&ie=UTF8&qid=1329431263&sr=1-12
Cheaper on WDC site but Out of Stock
http://store.westerndigital.com/promo/86120800
I'd go with 1.5TB models throughout: replace the 2 x 500GB which sound older and 2007 era? setup 3 x 1.5TB if you think you want 1.5-1.8TB for active projects on your internal drives (3 drive array)
Or there is this:
http://www.macperformanceguide.com/blog/2012/20120216_1-Hitachi-Coolspin-4TB.htm l

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