From what I've figured out, some countries have the second letter as a designator. Examples:
LATI - Tirana, Albania
LGTS - Thessaloniki, Greece
LBSF - Sofia, Bulgaria
EDDL - Dusseldorf, Germany (Deutschland)
LIMC - Milano, Italy
EPWR - Wroclaw, Poland
LFPB - Le Bourget, France
ENGM - Oslo, Norway
And the list goes on...
Yet, there are many that have no resemblance at all...
LWSK - Skopje, Macedonia
LJLJ - Ljubljana, Slovenia
EKCH - Copenhagen, Denmark
It could be a coincidence, I am not sure...
Somebody with more knowledge could tell us.