Rock, denied by Shane Lowry in a play-off for the 3 Irish Open a year ago, dropped a shot at his first hole of the day but responded with six birdies to be five under after 11 holes.
That put him one ahead of fellow Englishman David Lynn during the early stages in Perthshire, while a shot further back the race for a spot on Colin Montgomerie's Ryder Cup Team was hotting up as Simon Dyson and Edoardo Molinari put themselves in amongst the chasing pack.
But for McGowan things were not looking as hopeful - needing a top-two finish in the final qualifying event just to have a chance of an automatic place, he was four over par after eight holes.
Earlier this year he suffered knee and then wrist problems, but it is the trapped nerve in his shoulder which has now derailed his attempt to earn a debut at The Celtic Manor Resort in October.
The 28 year old, excused the eve-of-tournament pro-am on medical grounds, managed only four pitch shots on the practice range on Wednesday before calling a halt.
Despite painkillers and strapping he dropped shots on the tenth, 13th, 15th and long 16th, where he was in a greenside bunker for two, left it in and then missed from seven feet.
Even when he struck his tee shot to 15 feet on the 194 yard next he squatted down in clear pain and then got up feeling his shoulder and chest.
Sad though it was for him, it was good news for playing partner Miguel Angel Jiménez, who was in the hot seat of ninth on the points table.
Pushed down into the last automatic qualifying spot by Peter Hanson's Czech Open win on Sunday, Jiménez made a late decision to play rather than take the week off.
That meant missing his nephew's wedding - unless he misses the cut - but the Omega Dubai Desert Classic and Alstom Open de France champion was off to a good start.
Under threat from his fellow Spaniard Alvaro Quiros and English pair McGowan and Dyson, Jiménez birdied the 350 yard 11th, his second hole, and added another at the 16th when he got up and down from the same bunker that McGowan was in.
He three-putted the next, but came straight back with a four on the long next and at two under was two behind leader Rock.
Quiros was struggling at two over after losing a ball on the 16th and matching McGowan's bogey six, but Dyson moved to two under with birdies at the 13th and 15th.
The York golfer was mightily relieved at the next when a search was needed for his ball on the edge of the water short of the green, but he found it himself plugged in the rough and parred the hole.
McGowan battled on and even birdied the 533 yard 18th, but three over after ten holes was eight adrift of Rock and Dyson, whose Ryder Cup ambitions were still very much alive as he birdied the second and third after turning in 33.
Jiménez was two under after 12, but Hanson had dropped back to level par and Quiros one over.
Dyson, 12th at the US PGA Championship and fifth in the Czech Open the last two weeks, made it four birdies in six holes with a 25 footer on the fifth and with that became leader on his own.
At six under he led by one from fellow Englishmen Rock, Lynn, Richard Bland and Andrew Butterfield and also Scotland's Marc Warren. Winner of the title three years ago, he eagled the 16th to go joint second.
McGowan's problems were there for all to see again when further bogeys came on the fourth and fifth to put him four over again.