are the yellow stains rough to the touch? IF so they are scale deposits and explain where all the calcium went (ASSUMING that the water testing at Ace was correct. Ace Hardware uses the Lamotte Waterlink Express testing in many parts of the country--little square vials with dry reagents in the bottom that pool water is added to with a special pipette and then the results are either read in a machine or compared against color charts--and, while this is a good testing method, it has to be done properly so ask if the operator has passed LaMotte's certification test on the unit and ask to see their certificate. I personally know about this since I have the certification and it is to make sure the operator knows the limitations and possible interferences that can give 'off' test results and how to avoid them or when to use a different testing method). Also, there are some limitations in the LaMotte's calcium test and it can actually read low then the calcium is very high (above the range of the test which , if I remember correctly, is around 400 or 500 ppm)

Anyway, getting back to your stains... If they are rough feeling and yellow in color they are most likely scale deposits. If you can scrap some off with a fingernail (carefully so you don't damage your lner) and put then in a glass of vinegar and they fizz then they are scale (calcium carbonate).
You can try loweing your pH to 7.2 and keeping it there ( you really need your own good test kit to do this and I would recommend spending the money ont he Taylor K-2006 in the link in PoolDoc's signature for FAS-DPD test kits). Over time the lower pH and a lot of brushing might cause the calcium carbonate to redissolve. Be sure you do not lower the pH below 7.2 because liner pools can be damaged by low pH.

The problem is most likely caused by a combination of high calcium, high Total Alkalinity and high pH. If you have been following the computer printout from the DataMate software then you have been overdosing on the baking soda and your Total Alkalinity is probably too high. Also, as PoolDoc said, there is NO NEED for calcium in a liner pool. Calcium is needed in plaster pools.
Bad news is if the scale deposits are bad you might need to replace the liner (assuming the stains are scale). However, yellow stains are usually scale and the fact that your calcium 'dissappeared' reinforces this.