XP has 3 layers of tiles on the map. Chances are you have drawn with a blank tile on a higher layer, and that is the passability that's being checked.
The roof tiles and tree tiles can be copied/pasted in a large block, but only a part of that block actually has images on the tiles - the rest are blank. So if you DO copy the whole block and paste it, the empty tiles in the top corners are still there and they will be used for passage settings.
There are a couple of ways to find out if you've done this. One is to edit your tileset, find ALL the "empty" tiles, and paint them in a color that will stand out. Save it and re-open your map (if you haven't closed the editor, you'll need to go back to the Tileset in the database to see the new version of the tilesheet, and then go back to the map), and look for all tiles in that color. Then use the top left tile, which is the 'erase' tile, to draw over them and get rid of them.
If that doesn't help, you'll need to be more descriptive about what's going on. "Doesn't work" is the only information you've given us that's actually useful. What does "doesn't work" mean? Can you walk everywhere? Can you walk nowhere? Are there just SOME tiles that don't behave properly? Is it just one map, or all maps? As Andar said, screenshots will help out here, and highlight on them which areas have the problem and what the problem is in those areas. Otherwise we're just guessing (which is all I've done above).