I have just gone through this problem. It could be nitrogen. Nitrogen EATS chlorine like there is no tomorrow. I only realized this problem when my solar blanket well 2 of them literally deflated and sunk to the bottom of the pool as the bubble inverted and deflated themselves. These were 2 brand new covers so it was the pool water, one was on for two days only. No pool company here could figure out the problem as the water appeared clear, until I found an obscure reference to why the bubbles deflated on the internet.
"The most common sanitizer used in swimming pools is chlorine. When added to pool water chlorine carries out two main functions; primarily it destroys micro-organisms but it also acts as an oxidizer, destroying organic contaminants. One result of these chemical processes is to convert the active free chlorine into chloramines and other combined chlorine compounds. It is recommended that free chlorine levels should be kept as low as possible – between 1 to 3 ppm. Combined chlorine levels must be below 0.5 ppm. Should this ratio be allowed to reverse and the combined chlorine levels climb above the levels of free chlorine, then nitrogen trichloride gas is produced. A clear indication of this condition is an obvious chlorine smell and it will also cause eye irritation to swimmers.
Extensive tests have been carried out and the resulting factors of this condition indicated that in a relatively short time the air inside the bubbles was almost completely drawn out. It is believed that when nitrogen trichloride gas is allowed to build up under the cover, air will diffuse out of the bubbles causing them to deflate. Once the bubbles have collapsed it is not possible to reverse the process and a new cover will be required.
When this problem occurs it is very important to bring back the pool water to an acceptable level of chlorination, either by shock dosing and burning out the high levels of combined chlorine, or carrying out a partial water change before a replacement cover is introduced onto the pool. When shock dosing the pool water it is essential to remove all covers until acceptable chlorine levels are reached. The pool water must then be closely monitored to ensure that the combined chlorine levels are kept below 0.5 ppm."
The Pool company here was able to do their test and if you have one of the big test kits you can do it yourself when you have the three step chlorine test. You need to make sure the the Combined Chlorine is lower than the Total Chlorine. The way we fixed this was to shock the pool with 20 litres of liquid chlorine and then test the next morning. I guess the goal is to have the chlorine levels stay high for 2 days, if that happens you have the problem licked! The pool company here said that it could take from 20 - 140 litres of liquid chlorine to fix the problem but trust me that is better than a full empty and refill!
Don't worry I felt like a fool too every time I went to the Pool store and got told their was no chlorine in the pool. As PaulR states Chlorine is something that does have to be added regularly but if you have nitrogen you could put 5 litres (my normal Sunday night shock dose) in the pool and have a reading of zero 12 hours later.
Hope this helps because I know it had stumped me for awhile and the new covers were getting expensive!