Quoting aaron_da_killa
A bsp brush can be split because of:
- Another non-entity bsp brush is touching or intersecting it.
- The texture tiles, a 1024x1024 surface textures with a 128x128 texture at 1.0 scale will cut that surface up 8 times vertically and horizontally wherever the texture tiles.
It's also important to consider what compile tools your using as this is what can also cut your brushes up. Try using zhlt 3.4 if you aren't already.
I figured out what was causing all the mystery 45' lines everywhere, the texture (which was already scaled up to 1.5 at the time, but is now 2.0) was rotated 45', because I read a tip somewhere that rotating a generic texture will help alleviate the tile-iness