Open the WAD in a lump editor and delete the BLOCKMAP lump. Editors can only build that lump when the level fits in a 32768x32768 square, and when it doesn't they just leave the old one in. SRB2 can generate its own BLOCKMAP if it's missing from the map, but if there's one there it'll just use it no matter what, which causes quite a few issues if it's inaccurate, like the one you described.