LJ VRT officers can hold acting paid rank when filling an established post in a rank higher than their substantive - that's very common indeed - and currently also acting unpaid Flt Lt after 9 years (though that is likely to be abolished). When relinquishing such a post they are usually granted permission to continue to use their acting rank, now unpaid. Again there are moves to stop the latter practice.
So, an ATC Sqn commander is likely to be A/Flt Lt/Pd; VGS commander would be Sqn Ldr, etc. Probably what you encountered was the current boss and his predecessor; but the second Sqn Ldr could also be holding a post elsewhere (wing staff or CCF contingent commander).