Thank you for the reply Raymundo; I just changed the number of bad channels to match the bad channels from the resting-state recording and everything worked fine 
As the different number of bad channels (compared to the resting state bad channels) seemed to work fine with the good folder I assumed that this wasn't the cause of the issue - many thanks again and sorry for taking so much of your time.
Just out of curiosity, regarding your comment down below, what do you think may be the reasons that having a different number of bad channels just worked for this good folder by chance?