The reason I asked is because, in my experience, a lot of the problems at startup are due to a "race condition". Which is where too many processes are competing for processor resources and bits start to "fall off the edge", as it were.
The above being the case, I have found that if I have a problematic process occurring at login. I usually set it to manually load in some way via a startup command, often with a delay built into the command. So, for example, I might make a little script like the following:
sleep 2
killall mate-panel
mate-panel
And then run that as a startup script at login
However, I also think you could resize the panel using a script with something like:
gsettings set org.mate.panel.toplevel:/org/mate/panel/toplevels/bottom/ size 45
Obviously, you would need to change the above command slightly to reflect which particular panel you are referring to and the specific size.