Hi Sunnz,
Can you help clarify a couple things for me?
Are you utilizing standard Workflows or are you utilizing Case Creation rules?
The Case creation rules can drive the process to pull the records from an email queue and then bring them into Dynamics and create the case. You can also then use the routing rules to route the case appropriately based on specific key information.
You mentioned "I'm seeing with folder tracking is that some of the workflows fire and some won't". You are relating the folder tracking here with the workflows and I am not sure exactly what you mean on this. The folder tracking in Outlook / Exchange will be setup to track to the specific custom entity you created. It does track the message to this folder but then does not fire the workflow to create the case correct?
Overall if this is the situation that is happening I would not expect that you are firing them too fast as Microsoft should run the workflow for each of the activity records created.
Looking at your architecture, I would suggest maybe looking at a different approach.
1. Create 10 email addresses for the different types of messages that you were putting in the folder tracking (if they are different than the ones they are going to originally) and setup forwarding rules in Outlook to send to these email addresses or if you are manually moving to the folders then send to the forwarded email addresses instead
2. Setup Case Creation Rules attached to these emails that will create the cases in Dynamics 365 automatically. (docs.microsoft.com/.../automatically-create-case-from-email)
3. Use Routing rules to move the cases appropriately (docs.microsoft.com/.../create-rules-automatically-route-cases)
