Yes, um. PKL isn't based on this forum, but on the AHK forum. On the other hand you may not have an account there. Let's hope that Farkas looks in here, then?
Or, to spread your chances out you might try the SourceForge forum and/or the PortableApps one; although those topics seem fairly deserted.
However...
If you set layout = colemak, you should have a directory [main pkl folder]\layouts\colemak where the layout.ini is. Make sure you have the access rights for that on your running account. For instance, if you made the folder as admin a user might have problems reading it later?
Same goes for the pkl.ini file in the main pkl folder - gotta have the run rights for that too. But I suppose you have that covered.
If you only need the layout.ini itself, you could always run pkl in 'compact mode' - set 'CompactMode = yes' in your pkl.ini and put the file(s) for the colemak layout in the main pkl folder. See if that does the trick, if it's a workable solution for you.