I have been chasing this problem for about 5 days and have finally found the issue. I have searched the forums and have found that many people have this problem too and did not see this solution so I hope that this helps them.
If you find that your layout looks differently at your deployment system than your development system and the problem seems to be that your labels…field and/or panel are not correct or you find that Studio changes do not want to stick, check the files in the ~custom/Extension/modules//Ext/Language directory. If you have many several deployments and you have named your customization zip files differently (I was putting a timestamp on them to make them distinctive), you may have found the source of your problem. The files in this directory are applied in some order (I believe alphabetically) and depending on how you name your files, you may not be getting the final result that you want. The way to determine which labels are resulting from the build is to look in the custom/modules/,module name./Ext/Language/en_us.lang.ext.php file at the $mod_strings for the label or labels that are having the issue. This will tell you the final result after the build/repair. I deleted the confusing entry from the ~custom/Extension/modules//Ext/Language directory file and repaired and my problem is fixed. Yay!
Dianna