Hi!
Yes, this ought to be addressed by the package upgrade, probably through debconf, or modify gtklp so it sees this, then does the update automatically. I'm packaging 1.0pre2 now, and it ought to have this.
I realized the problem after the last modification of the config-files. The next time I change them, I'll also implement some kind of version check *in* these files to avoid problems in the future. But for now, I don't really have a better solution than a warning when old config-files are found....
wys SirTobi