if you haven't you might want to copy the effect into the side (that's what you're doing i assume), maybe rename it to differentiate.
also, try cleaning and munging. sometimes my effects wont update and cleaning seems to help.

Frag: No added anything to my map, it is completely stock. Also I turned light bloom off, fiddled around with the lighting quality, but no dice. Nothing changes it

This reminds me of how, with effects, if you use an unknown texture for them they'll come out as squares.

Try using a stock laser texture, not a modder-made one such as in the BFX assets, but one that came with the Modtools, and just reskin it.