I have the same problem. However here the details again, maybe there is a new bit:
when applying the skin the bootskin pro program said it has been successfully applied. Then restart the program and its still the default windows bootskin active.
Rebooting leads to that blue/green color mess (btw: this is the same bootskin you have when restart from hibernate mode).
I have Vista Business 32bit, UAC active, all locales are set to German (even those non-unicode stuff).
Strange again: BootSkin Pro tells me that it is version 1.00.035. Impulse doesn't tell me something about any update, even after refresh.
So I uninstalled, reboot, installed again -> same version, same problem.