In reply to jonny taylor: Have you tried contacting Citizens Advice Scotland? There seems to be a separate web site for the direct contact service:
http://www.citizensadvicedirect.org.uk/ - they offer phone, e-mail or web chat.
The first link you posted seems quite clear that the monies you have paid now should be converted in to a properly protected tenancy deposit, or else returned to you and a protected tenancy deposit taken instead.
The Shelter web site linked from your Citizens Advice link could hardly be clearer! It says in BIG red letters: "Letting agent fees are unlawful in Scotland" - just in case you hadn't understood "Any fees charged by the landlord to create or renew a tenancy are illegal" on the Citizens Advice web site.
Given the apparent discrepancies in the information you have now been given about the identity of the landlord, I'd be starting to have serious reservations about this whole affair. I can understand that it's difficult if you have to travel to view properties but how happy are you going to be living in a place with the constant feeling that the landlord is trying to rip you off? Do you have a fixed deadline to get moved in eg starting a new job? Even then, you could consider putting the bulk of your stuff in to storage for a few weeks and B&B/hostel it until you find somewhere proper to live. (Some employers will help find temporary accommodation for new staff, sometimes even other folks in the same company will put you up as a lodger for a while.)
This is quite interesting to me because a relative recently had to back out of a tenancy at the last minute when their property sale fell through, and they lost a 'deposit'. It hadn't occurred to me that it might be recoverable. I shall suggest that they get advice on that.
Good luck with getting settled in, wherever you end up.