Gmail has 5 different inbox types, that can be configured to handle messages and unread messages in different ways. To make sure that Wavebox reports the correct unread count and notifications, you need to ensure it's configured in the same way as your Gmail account.
Find out more about different Gmail Inboxes
When adding your account for the first time you'll be prompted with different options. If you change how you use your Gmail account, or weren't sure at the time which option to choose, you can easily change it later.

Changing your Inbox Type
If you dismiss the welcome prompt or want to change the Inbox Type later, you can do this through settings...
First check which Inbox Type Gmail is configured to use, click on the Settings cog in Gmail, in the Quick Settings, Gmail will show which inbox type you're using

Now we need to tell Wavebox to use the same Inbox type. Open your Wavebox app settings, by right clicking on your Gmail app in the left/top-toolbar and clicking App Settings:

Finally find the Inbox Type setting under the Gmail heading and change it to be same type as what you're using in Gmail:

If you want to find out more about different Gmail Inboxes, Google has some excellent advice on Choosing the right inbox type.
Special cases
The steps above work for the a majority of Inbox Types and setups that Gmail offers. There are some that may need a slightly different configuration to this. After setting your Inbox Type, if you're still seeing different unread counts and notifications it's worth checking through these cases to see if any apply to you...
1. Default Inbox, with only the Primary category: use Unread First
You're using the Default Inbox
setting in Gmail, but have disabled all categories apart from the Primary
one (this cannot be disabled).

In this case, Gmail treats your Inbox as Unread First
and doesn't apply the Primary
label to any incoming emails. In this case, set your Wavebox Inbox Type to Unread First
.
2. Priority Inbox, with a different Gmail Unread count configuration: use Unread First
You're using the Priority Inbox
setting in Gmail, but have chosen Unread items in the inbox
as your unread count

In this case, the Gmail unread count is taken from the total amount of unread items in your inbox. Set your Wavebox Inbox Type to Unread First
Further troubleshooting
If you're still seeing an incorrect unread count, even after setting your Inbox Type and checking the special cases there may be some other scenarios that cause an incorrect count
Signed into multiple accounts
If you've signed into multiple Google accounts in a single profile, Wavebox will only show the unread count and notifications for the first account. You can check this by clicking on your account icon in Gmail (top-right). If you see multiple accounts listed, you're signed into multiple accounts in the same profile...

To resolve this, click "Sign out of all accounts". On the following screen use "Remove an account" to remove the one you no longer need and sign back into the account you want to use...

From here, the unread count should reflect more accurately how many unread messages you have in your inbox. To add a second Gmail account, use the plus button in the sidebar and ensure you add this account to a new profile. (This will be the default option during the add process).