Sure thing - Since I use EVGA Precision or MSI Afterburner depending on which brand of card I'm running, I'll simply stick with MSI-A for this example (The process is identical for each utility).
1) Start MSI-A and set clock/core/power/fan settings. I use a saved profile for this.
2) When WinMiner starts actively mining, it wipes out my configuration
3) The configuration in MSI-A actually remains, but I cannot re-apply without a small change, so I make the small change and re-apply.
4) Winiminer changes miners/coins/etc - I make the small change and re-apply as in #3.
If there were a way to automate this process of setting the frequency/clock/etc from the command line I could have it change out every minute and simply alternate between 81-82% power and be happy about it (this wouldn't really give it enough time to get super hot or out of sync, but it does seem that some of the applications do support options for power settings (Specifically Claymore).
When running MSI-A/EVGA-P, the 'monitor' window and the temperature is what I'm using to indicate that my settings are simply not being held on to, despite the window of the system not being appropriately adjusted as well.
If you'd like for me to set up a screen sharing session to demonstrate this to your team, please ask them to respond to my support request and I'll happily do so. It only takes about 2 minutes to demonstrate this.
No promises - but we will have a deeper look and see what can be done to help