Auto build is not triggering for apps created using aws js v3 SDK

### Before opening, please confirm:

- [x] I have checked to see if my question is addressed in the [FAQ](https://github.com/aws-amplify/amplify-console/blob/master/FAQ.md).
- [X] I have [searched for duplicate or closed issues](https://github.com/aws-amplify/amplify-console/issues?q=is%3Aissue+).
- [X] I have read the guide for [submitting bug reports](https://github.com/aws-amplify/amplify-console/blob/master/CONTRIBUTING.md).
- [X] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.

### App Id

d3hpthrkzw4m7o

### Region

us-east-2

### Amplify Console feature

Build settings, Webhooks

### Describe the bug

I have created an app using AWS js v3 SDK. Firstly I have created an app then I have connected the branch. After these steps automatic build was not triggering so I have created a webhook and created a job for the first deployment. It worked as expected. Later I have added some dummy code so that I can push the changes to GitHub and it will trigger an automatic build on amplify but it didn't work.
Later I have created a new app(App ID - dmq2wgvwomfo3, Region - us-east-2) from amplify console and connected the same repository. I have removed the dummy code mentioned above and pushed the changes to Github and automatic build triggered on a new app but not on the previous app created using SDK.
I have checked the webhook status on GitHub and it's showing status code 202 for both webhooks.

Apart from this, I noticed one more thing when I have created the app using console there is no webhook getting displayed in the console and on GitHub we have webhook of that app.

### Expected behavior

Apps created using SKD should behave the same as apps created using the console. If we have connected one repository in more than one apps then after commit it should trigger build on all apps.

### Reproduction steps

1. Create a new app using CreateAppCommand
2. Connect branch using CreateBranchCommand
3. Create a notification for the automatic build using CreateWebhookCommand
4. Start the first deployment using StartJobCommand
5. Add dummy code and commit the code
6. Webhook status on Github shows 202 but the automatic build is not triggered on amplify

### Build Settings

_No response_

### Additional information

_No response_

Start by reproducing the flow with CreateAppCommand, CreateBranchCommand, CreateWebhookCommand, and StartJobCommand, then compare it with the console-created app in us-east-2. Use the GitHub webhook status and Amplify build history to identify where the SDK-created app diverges; done means commits trigger builds consistently for both apps and webhook behavior is aligned.

Written by the indexing model from the issue text.