Leaks as holes in map? If you have no skybox and have 'holes' in map than its not holes. Its overlapped brushes, just 'cauze of mapper inaccuracy. Also if you using different girds with common tools and dont care about precise brushes align, its also can be source of errors. Many clip attempts with different angles on one brush can accidently produce too small triangles, which also can be source of bugs. If you want - you can post screenshots or PM me a map so i can take a look. As i told i cant say anything without looking into map. =D
UPD Sorry if i understand ur post wrongly. U fixed it or not? If fixed - dont forget edit your post and mark it as [solved]. =)