Message Control Bypassing "Suppression" when Reloading Service Engine

Message Control Bypassing "Suppression" when Reloading Service Engine

I am running zenon 11 Built 101682 64-bit.

We have a system with Message Control operating generally as desired with SMTP emails working properly.
The issue is that when we reload the Service Engine to apply the updates via a standard "Reload" function, the service engine often generates new emails for a bunch of pre-existing limit values which haven't changed state but are sitting in the value to generate an email. These new emails get generated even though the Message Control screen still shows the Alarm Groups that these points are attached to as Suppressed. The CEL does not show the limit value being triggered, but it does show the email being generated (we have all Message Control messages being logged for the time being). The message control screen also shows the new backlog of emails that it is working through.

Our emails are all triggered through Email Functions called from variables via the Limit Value "Execute Function Instantly" property. We are configuring email suppression via the same limit values which have the function calls all being attached to Alarm/Event Groups. The Alarm/Event groups are suppressed and un-suppressed through the template "Message Control" screen. We do not have email acknowledgements or anything; zenon is purely sending emails.
In our procedure, we ensure that we suppress all groups before pushing any updates from the Engineering Studio and refreshing the Service Engine. We do not currently use the "Send Message: Deactivate" or "Send Message: Activate" functions since the Suppression options are multi-purpose (allows disabling notices for sub-systems as needed, and we also had hoped to use them for preventing emails on reload).

Does anyone know what is going on here? Do we need to make a Script for the "Reload" function which also calls the "Send Message: Deactivate" and "Send Message: Activate" functions? Or do we need the "Send Message: Deactivate" and "Send Message: Activate" with some sort of time delay to ensure the Service Engine is fully up and running?