Excel custom Add-In not loading when instance of E

Question

I have created a custom add-in for Excel and for the most this work fine without any issues.

However, we have a 3rd party application where we can select the option to "Open In Excel". This then loads a new instance of Microsoft Excel with a load of data populated from the application, but does not load the custom add-in.

If I go in to the add-ins option, I can see that Excel still seems to think that the add-in is enabled but I can see that it is not because the macros are not imported to workbook.

I can disable and then re-enable the add-in and it will work just fine. I can also open an Excel document or a new instance manually and it will work as expected. It only ever seems to be an issue when the instance of Excel is opened from this 3rd party application.

I assume that this is because the add-in is bound to my account and the process is being started by another account even though task manager sees it as being a process ran by myself.

If anyone has any ideas as to why this is happening or how to resolve it, I would be very grateful to hear.