ppm is parts per million.. With typical ppm meters this is actually calculated froma measured resistance, and compared to the equivalent resistance of a NaCl solution at whatever ppm.. (Yep, a ppm meter is basically a really sensitive AC ohm meter)..
Pools confuse things further by separating pH and alkalinity.. pH is the result of the net average number of acidic and basic compounds where as alkalinity is the total concentration of carbonate (a basic compound).. So If you had 1000000 particles of acid, and 1000000 particles of carbonate in there, the pH would be 7.0, but your alkalinity would be 1000000 (these numbers are imaginary BS btw).. And if you had water with no acid and no carbonate, pH would be 7.0 and alkalinity would be 0..
On that note, the more acids/bases at a given pH, generally the more stable it will be in that range.. pH is all about ratio, not so much total numbers.. (On that note, I don't know how strong 40ppm alkalinity is, or if its even real ppm or what).. But it does sound like some kind of alkaline buffer is the culprit.. Do you use phosphoric acid as a pH down?? It is the best because it reacts with carbonates to make new compounds that tie up the whole acid/base thing that will buffer the pH between 6 and 7 rather than higher than that like carbonates alone tend to.. Other things like citric acid will just affect that pH acid/base ratio, not form to stabilizing compounds.. Eventually things should improve doing what you're doing with phosphoric acid, wheras with most other pH downs you'll just be temporaily adjusting the ratio.. If you are using phosphoric acid and things aren't getting better then I'm at a loss..