Hello Suresh
You need to control chain execution in BW as well once it is being triggered through event, for example by adding wait time in the first step of chain or by adding an ABAP program step which will check if the previous run has been completed after which it will proceed with data loading and activation.
However in order to make some precise suggestion please share what is the runtime of each chain and what is the time gap between execution of each chains for various regions.
Ashish