Are you using Stand-alone controller or Performance center ?
Runtime setting for groups in Controller get stored in scenario file rather than in script file. For initial adding of the script they get imported from script file and you can change them in scenario file which won't change script settings.
On PC there are few bugs in UI if you want to copy group settings from one group to other as well as it won't allow changing Block %-tages if you are using Blocks in your runlogic etc. So be careful and make sure changes you saved or checked-in are the one's you desire before running your actual tests.
Tnx!
