As of this page http://wiki.openstreetmap.org/wiki/Tag:boundary%3Dadministrative the administrative levels in Slovakia are:

admin level 6: Borders of Bratislava and Košice

admin level 8: district borders (because of this you see okres.... you see only district capital cities)

admin level 9: town, village or autonomous town in Bratislava or Košice.

So you should probably use something like that for Slovakia:

mkgmap:country=SVK & mkgmap:city!=* & mkgmap:admin_level6=* { set mkgmap:city='${mkgmap:admin_level6}' }
mkgmap:country=SVK & mkgmap:city!=* & mkgmap:admin_level9=* { set mkgmap:city='${mkgmap:admin_level9}' }
mkgmap:country=SVK & mkgmap:city!=* & mkgmap:admin_level8=* { set mkgmap:city='${mkgmap:admin_level8}' }

I tested it. It worked, but several streets are missing in the index. I have no idea why.

In Czech Republic probably

mkgmap:country=CZE & mkgmap:city!=* & mkgmap:admin_level8=* { set mkgmap:city='${mkgmap:admin_level8}' }
mkgmap:country=CZE & mkgmap:city!=* & mkgmap:admin_level7=* { set mkgmap:city='${mkgmap:admin_level7}' }

would be the best option. I did not test.

Marek