The only issue I've had with mine (Thunderbay 4) is that the slightest of movements seems to disconnect Thunderbolt. Now mind you, a box full of spinning hard drive platters isn't something that I move around often, but during the initial arrangement I did manage to disconnect several times.
Tried a couple different Thunderbolt cables, and seems as if the ports on the unit as just a tad too shallow. That said, a non-issue once the box has been put into its final resting place on my desk, and I used a stick on cable hold down and a loop of cable as 'slack' to prevent it from disconnecting inadvertently.
I own their Helios II Thunderbolt box as well, and wish the Thunderbay came with the similar cable clamp to keep things in place.
I was skeptical of SoftRaid, as I was initially unaware how long the software had been around and the performance of "software" raid in general, but I ended up being really impressed with it and ended up buying a license (even after the recent +$50 price increase).