aquaguy:
Please tell us what addatives you are using. If PH and and Ca are good, and the animals are good, I wouldn't worry.
trybka:
I observed the same in my tank - adding liquid calc lowered Alk and PH too.
Here is my explaination (it is sensible, but maybe not 100% correct). Basically, as Calcium is used by animals, or precipitates out, It does so as Calcium Carbonate. This removes carbonate (ie Alkalinity) as well as calcium. Liquid calcium is usually Calcium Chloride, and exchanges your Alk (Carbonate) for extra Chloride ions (I don't know what this effects).
Your makeup water in the fish only (if you didn't use RO) could have had high PH or Alk. When I did freshwater, my PH and Alk of the were way off the top end of the charts (but I had well water, and kept cyclids). Also, some salt mixes are less consistant.
Carbonate can form from Co2 (in our atmosphere), and this lowers PH. Carbonate can release CO2 and raise PH. This balance is what makes carbonate 'buffer' the PH. If your PH is off, your Alk will be too.