Chlorine is very effective in ...

Chlorine is very effective in inactivating E. coli in a drinking water context, less so in a wastewater context.  The main issues affecting the effectiveness of chlorine in a wastewater context are the presence of particles, which can shield the E. coli from the biocidal effects of chlorine, and the presence of organic compounds that may preferentially use up the chlorine (i.e. exert a high chlorine demand).  It is a little bit unusual to be using chlorine gas in a wastewater context, normally hypochlorite solutions are used.  Anyway, if the free chlorine residual is 5 mg/L, then an E. coli result of >2000 orgs/100mL is very unusual, and, as other respondents have noted, you might like to look at sample contamination.  With that level of suspended solids and that much free chlorine you should be able to achieve a result of <100 orgs/100mL.  Best of luck with resolving the issue.