This is a little bit weird. Did you do some Sandbox testing by any chance?
Are all the Stripe plugins and addons updated to the latest?
Lets enable the debug logging so we can see what exactly it is doing.
Using the Debug Log to Solve Transaction Related Issues on a Site
After every transaction, can you please check the log file and match the orders in the orders menu to make sure all matches? If you find one is not going to the orders menu, please let us know so we can read the log file and see what is going on.