1st issue. In radiant my maps skybox is set to night time. The lighting and everything is fine until I get into the map to test something and its still basic daytime. No clue what im doing wrong.

2nd issue, just looking around the map I seem to get these sort of "burn ins" of the map and my weapon, sometimes they go away if I just look at the sky or something and sometimes not, heres a picture http://imgur.com/a/ArSur

For the first issue, make sure the worldspawn settings aren't changed, only change the ssi on the sun_volume.
Worldspawn should have

skyboxmodel / skybox_default_day
ssi / default_day
wsi / default_day

Sun volume should have in the Light State 1 group

ssi1 / "name of ssi"

Without quotations.

For the second issue turn off ambient occlusion