Ok look iv been using Cubase for the last 6 years, i think i know the program how to setup the midi channels. in a nut shell it was because i installed Sound Trap Software. it messed up something in my USB drivers in windows, but only when it was sending midi to cubase and protools. i dont know how or why it did but seeing as i re-installed my windows last night and everything is back to normal part from the fact i have to install my plugins and presets again.
it was a driver issue i was having it started with the STDRIVER64.sys
from what i can tell, it f**ked up my usb driver stack inside windows, but again only with cubase and protools.
a fresh install has done the trick, but a very costly one 
dont mind my bad spelling atm i have just woken up after a long night of installing and iv still got another 2 days and nights to go