Hi
there are several things in play here and based on the information your provided i can come up with some possible solutions:
Make sure you are running FMRTE as Administrator (right click in the FMRTE icon and select "Run as Administrator")
In case you are using the Heal and Inspire team buttons one common "issue" is that since Fitness and Condition were included in the Freeze function its common to see some users trying to heal and inspire there teams but forgetting that they froze the entire team while back and what happens is that FMRTE saved the Fitness and Condition values back then and when you try to heal your team FMRTE resets those values since the players are Frozen.
All you need to do is to UnFreeze Heal\Inspire and Freeze the players again, this in case you wan to keep your players Healed and Inspired all the time other solution is to add Fitness and Condition to the ignore frozen attributes list in your Settings -> Freeze Settings Tab
Let us know if any of these helped you, so other users in the same situation can find there solution