Disk utility false "failed" disk errors

Hello, I'm really hoping someone can help me solve this problem.
I have an iMac (see specs below) connected via Thunderbolt to a LaCie 2big RAID drive (with two 3TB internal Seagate drives set up as mirrored RAID slices). Both the iMac and the LaCie drive were purchased brand new in 2012 and worked flawlessly until April 2014. In April, one of the LaCie's two internal drives failed and could not be rescued using Apple's Disk Utility. Since the LaCie unit was still under warranty, LaCie replaced the affected internal drive at no cost. Since then however, Apple's Disk Utility has been giving me a "failed" disk warning on the same internal drive about once a month. The first time, LaCie simply directed me to reformat the drive and the problem went away. But the same problem has appeared roughly every month since then.
I sent the entire unit back to LaCie for diagnosis and they told me that the drive is perfectly fine. In other words, it's a software failure, not a hardware failure. I was told that Disk Utility was giving me false errors, possibly caused by the iMac going into sleep mode and not ejecting the disk properly. They said they've seen it before, but Apple has not yet released a patch for it. Since receiving the drive back from LaCie, I've changed the iMac's energy saver settings to prevent it from going to sleep after any inactivity. However, the same drive failed again this morning.
The only solution LaCie has given me is to wait for Apple to release a patch and in the meantime, reformat my drive whenever the "failed" warning appears to clear the problem. However, I have more than 2TB of data on this drive and the process of backing it up, reformatting the disk and copying all of my data back again typically takes more than 20 hours. I simply cannot afford to keep doing this every month. LaCie seems to have washed their hands of this and pointed their finger at Apple's Disk Utility. My questions is, has anyone else had similar problems? And if so, what is the solution?
Hardware Specs:
27-inch iMac, Mid 2011 (3.1 Ghz Intel Core i5, 12 GB RAM)
LaCie 2big 6TB Thunderbolt RAID disk (set up as two 3TB mirrored RAID slices)
Thanks,
Mike.

Permissions you can ignore on 10.5 and 10.6:
http://support.apple.com/kb/TS1448?viewlocale=en_US
Using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard changed the location of a number of system components.
As long as you see, "Permissions Repair Complete" when it's finished... you're done.

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    I'm backing everything up right now, but I'm wondering how accurate Disk Utility is. The drive that I have in here is a non-Apple-installed 250 GB Western Digital that's been in here for nearly a year. Is it possible that the drive is failing beyond repair already?
    yes, it's quite possible.
    If so, is there any way to see the full extent of the damage and attempt to repair it before I go out and buy a new hard drive to replace it with?
    check the SMART status in disk utility as suggested. if it says anything but "verified" it means that the drive is expected to fail completely and you shouldn't try to repair it. If it says "verified" It's possible that reformatting will fix it so you can try that. this will wipe all the data on it so clone it off first as gbullman suggested. BTW, most drives come with manufacturers warranty longer than a year and you should be able to replace the drive. that's what I would recommend.
    Thanks for all the help and the fast responses!

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