First, it seems WINE has a problem switching refresh rates back after using full-screen applications.
Second, you could write a BASH script to do it for you. After all, if you have to do something more than twice, write a script.
Third, if you're using an nVidia card, it's ENTIRELY possible that you're running at the proper refresh rate, but the OS is reporting it to you differently.
Add the following to your xorg.conf under the device section:
OPTION "DynamicTwinView" "False"
Although I've never bothered to see if it makes a difference, be sure to separate the columns with the tab key.
That should fix the way it reports the refresh rate to you.
Let us know if that solves the problem!