Ok, seems that the root cause is Flowable UI, that is sharing the same database with my application. The reason? because I am using Flowable UI to update the process and deploy the app using its UI.
I think that when I restart my application, Flowable UI tries to execute the process and it does not have my custom bean deployed. Then it cancels the process.
According to forum I can disable the flowable UI execution. Then adding to flowable-ui.properties the next line:
flowable.asyncExecutorActivate=false
Fixes the issue