Essentially, FBU is right: you need to get your chlorine up, and keep it there for awhile, and THEN see if you still have a problem.

We encounter many 'mystery' problems that go away once users do just that. Usually, the problem is resolved fairly quickly that way; sometimes it takes weeks rather than days.

Unfortunately, we often don't know why.

The level of chemical analysis that would exactly answer the "What?" and "Why?" question is almost always out of reach, not only for the pool owner, but also for us. So we have to be satisfied with solving the problem, without necessarily understanding its orign.