Will need some code snippets to dig further... There are some similar answers including:

• networking issue / VPN
• BOTO3 variables where you can set things like cli-connection-timeout which might help
• Multiprocessing in Python issues
• Number of other issues where things like packet drops / API taking too long, etc

Questions to ask:

• Are they all in the same VPC?
• Is there any difference between scripts?
• Is there any data skew (where some files are much larger than others)
  • If you're doing some processing on input files, and the input files are all 200Mb but the transformations create new data, those transforms might create skew in final output but idk
• Are you sure they're all on-demand and not being dropped as spot instances?
• Lastly are you using long term connections throughout? Like do you have the following below:

cnxn = boto3.connect()
process_data_for_a_while()
cnxn.upload(file)

If you do then maybe the cnxn is too long lived