Hi,
I think this is another incarnation of a known issue with re-running a macro multiple times: https://sft.its.cern.ch/jira/browse/ROOT-9014
In your case I suggest you load the macro once with .L start.C and then execute the function as many times as you want by calling start() explicitly at the prompt.
For better performance you might also want to compile the macro once before executing it many times with .L start.C++ (the ++ specifies you want to compile it) – then you can always execute the function at the prompt with start(), but it will have compiled-C++ speed instead of interpreted-C++ speed.
Cheers,
Enrico