with a CYA of 99 ppm keeping your FC at 5 or 6 ppm should insure that the nitrates are not a problem in terms of algae blooms (which are the only problem they might cause, btw.)

If you are not holding chlorine then you need to shock the pool (I would suggest using bleach -- or liquid pool chlorine if available in your area -- since it is what your SWCG produces) and get the FC up to about 25 ppm (which would be about 13 gallons of 6% laundry bleach--about 18 of the 96 oz jugs commonly found these days OR about 6.5 gallons of 12.5% liquid pool chlorine/shock or 8 gallons of 10% liqiud pool chlorine/shock. This should be enough to kill whatever is consuming your chlorine and your cell should be able to keep up with the chlorine generation again (assuming the system is working properly).
http://poolsolutions.com/gd/best-gue...ine-chart.html

HOWEVER, before you shock please test the water with an OTO test kit (sold as the 2 ways chlorine/pH test kits that use liquid reagents and have a chlorine comparator with yellow color blocks)
Your pool store is most likely doing DPD testing for chlorine and DPD can bleach out at high FC levels (OTO does not but only tests total chlorine). If the sample you test stays colorless then you have confirmed that there is no chlorine in the water. if it turns yellow, orange, or bronw you have chlorine (high chloirne in fact) and the pool store test is bleaching out. Please post your results so we can take it from there.

Also, you might want to collect some water from the cell itself when it is on to make sure it is making chlorine. Test this water yourself with an OTO test kit (comparator has yellow color blocks). If it turns yellow, orange, or brown your cell is working and the shocking I suggested above should do the trick. If it stays colorless your salt system is not working and you need to call for service (it might not be the cell but the control unit.)

Finally, stop depending on pool store testing! Get yourself a Taylor K-2006 test kit and test your own water. You might also want to invest in a tube of Aquachek salt titrators (test strips) or a Taylor K-1766 salt test kit to keep tabs on your salt level.