He wouldn't be troubled again when the red flags were deployed 15 laps into the 30 lap race, the decision then being taken to award half-points as the race had not reached two-thirds distance.
After pulling a remarkable move on Walker around the outside of turn one, Ellison was also able to get the better of Cooper to move into second position, although the early conclusion to the race prevented him from producing a repeat of his somewhat fortuitous race one win.
Unfortunately for Cooper, he was unable to maintain his early pace, dropping behind Walker, who made it a second podium of the day for the Henderson/Motorpoint Yamaha, and John Laverty, who produced his and the Buildbase Kawasaki's best ever result in fourth position after a late charge.
Nonetheless, Cooper held on for an outstanding fifth place finish in what remains just a one-off outing for the Superstock rider and team, the youngster taking a comfortable Cup victory in the process too.
With the likes of Stuart Easton retiring, Simon Andrews struggling with his spare bike and Hill having no wet weather experience on his Suzuki, Michael Rutter was able to put in another excellent result for SMT Honda in sixth position.
The Mallory Park race winner of 2008 might have fancied his chances of finishing higher had the race gone the distance, but his result – which backs up the cash-strapped team's best ever BSB finish of fourth in race one – is likely to do wonders for their chances of staying in the series.
Karl Harris endured a quiet race in seventh to get some much needed points on the board, ahead of a conservative Hill, while Steve Brogan posted his second good top ten finish of the day in ninth after riding through from 23rd on the grid.
Julien Da Costa, David Johnson, Tristan Palmer, race one podium sitter Graeme Gowland, Peter Hickman and Andrews completed the points.