It appears the true root of the problem has been for users with an English version of Vista that were using a non-US locale (such as the UK). Unfortunately, the code that was looking for the location of the winload.exe.mui file ended looking in the wrong folder because it was assuming there would be a folder for that locale on the system, which there is not always. However, there has been a beta released that should address this issue. Please let us know if you are still having the same problems and whether you're using an English version of Vista or some other language version, and what locale you have set.
Update: There is a new beta that's been published for BootSkin Pro that should help alleviate some frustration. However, there is one thing that has been discovered that will break BootSkin that is out of our control and is squarely on the shoulders of the user. In the Regional and Language Options menu under Control Panel, there is the Administrative tab, under which allows you to change the "Language for non-Unicode programs" locale. If this is set to a locale that you don't have a language pack installed for, then BootSkin won't be able to find the correct resources to edit. This isn't a "bug" necessarily in BootSkin, so much as the way that locale settings are handled in Windows. Please let us know of any further problems that changing this setting to the "correct" locale doesn't fix. For users with English versions of Vista, you may have to set this locale to "English (United States)" if it isn't already. You should be able to change the settings under the other tabs without incident so long as this setting under the Administrative tab is "correct." Thank you for your patience!