thanks skylais for the reply.
when i boot up it goes straight into windows repair enviroment but i can access a cmd prompt through the advanced recovery options.
i tried to run the scannow but it wont let me as it says that it cannot be performed as a system repair is pending.
im back to running start up repair,the last time i ran that specific scan it was over 24hrs and didnt complete.it does say on the dialogue box thats its checking disk for errors.this might take over an hour to complete.
the progress bar is moving so maybe its best to wait it out?