[mkgmap-dev] missing several streets in index

Hello, I am struggling with problem of missing several streets in the index. I use mkgmap r2661 with geofabrik extracted data for Slovakia. When I compile map of whole Slovakia with location-autofill=is_in,nearest I miss some streets when searching in my GPS device. I suspect it is somehow interconnected with geographical location. I for example miss streets Trenčianska, Turčianska and Oravská in Bratislava. They are very near of each other. I tried to compile map of extracted rectangle cca 1x1 km in tha area, and in that map they are in the index and are working properly. I still cannot find the cause of this problem. Any suggestions? Thanks Marek