Yeah, alk does seem a little low but before you make any adjustments be sure to confirm that your getting an accurate reading. Alk levels are a singnificant factor in the health of a tank and making changes when they aren't warrented (from inaccurate test results) can be quite detrimental. IMO, 6.7dkh is bordering on an fine line that can lead to mass chaos if its allowed to slip down a bit more. However, many people that run a low nutrient system through bacterial proliferation often run a steady alk somewhere between 6.5 and 8 dkh. Regardless, if your other animals are looking healthy, then the alk level is sufficient and I wouldn't be looking towards that sole factor to be the cause of your problems - Unless Johns params are very different from yours. If John maintains an alk much higher than yours then the nem may be a bit upset from the drastic change in conditions. It sounds like you got some other items from John as well and if they are doing OK then again I wouldn't look solely to your alk level as being the problem. In addition, I would suspect stony corals would be much more susceptible to changes in alk levels and a nem would be less affected unless the alk was so low that it was significantly affecting your pH.
What other livestock did you get from John and how is it reacting?? From my experience, a nem is much quicker to respond to a decreased water quality then most corals.
What kit are you using to measure alk??
What are you using to measure salinity??
My first guess at why this nem is irritated (without seeing your tank) would be excessive nutrients/poor water quality. A cycled tank should never have any detectable ammonia unless there is a massive die off or some significant event occurring. That leads me to think the test was either misinterpreted or gave a false reading. If your other animals are doing fine then you don't have any ammonia.
What kits are you using to test N and P?? Nitrate hobby grade tests are often incredibly inaccurate and phosphate tests are often misinterpreted due to a very faint color difference between very high P and undetectable P. Photometers are truly one of the most realistic (hobby grade testers) for getting realtively accurate results (however even they are susceptible to user error and other variables that can affect readings). IMO the most effective means of measuring your nutrient levels (N and P) is simply visualiation of the tank inhabitants and the amount of algae growth. If you have browned corals (excess zooxanthellae growth) and anything more than a little algea growth then you have excess nutrients regardless of what any test kit will tell you. Test readings can be skewed by the action of algea and zoox quickly uptaking the nutrients from the water column. The next question is - Are the water parmams causing poor enough water quality to have a nem react so negatively? Tough to say without a visualization.
My apologies for the long post. I'm trying to cover a lot of possibilities of what could be wrong and trying to explain my logic at the same time. Like I said initially there could be 1,001 variables causing this.
My suggestions:
1) Stop moving the nem. Even if your frag tank is plumbed into your main tank and exposed to the same water, then it will still likely be exposed to another variation in lighting conditions thus causing it to photoacclimate and expend energy doing so. If the frag tank is it's own separte entity and has different water params then that's yet another stressor but if it's already there then just leave it there becuase moving it back will cause more stress.
2) Let's hear what John maintains his params at. If they are very different from yours then it may be that the nem is slow to acclimate to your tank conditions. It may or may not come around (considering this is a clone of the indestructable FVRC RBTA I think it'll be just fine).
3) Give yourself a good evaluation of the water quality. I think visualization with attention to what signs excessive nutrients exhibit is better than any test kit.
Do you have any other nems or have you tried adding any nems in the past??
How long has the tank been set up??
Keep us posted and we'll keep trying to help.
Jeremy