Anyway to disable cyrodill quests while in si? Seems when i come back to cyrodill people dont give quests or anything.

This can happen if you console coc back to Cyrodiil from SI - or use mark/recall spells that doesn't update the variables correctly. If so, you can go back to SI via the portal and return to Cyrodiil via the portal - that should updade the PC position properly. See http://www.uesp.net/wiki/Shivering:Glitches for more on this. Also, some mark/recall spells work fine - Astral Mark/Recall in Midas, for example.