Mr Align, winner of four of his previous five races, was a beaten horse 800m out and dropped out from attending the pacemakers to finish second to last, 50 lengths away.
Stewards questioned the riders of both horses, Isaac Lupton (Counter Punch) and Daniel Oakden.
Both blamed, in part, the better-than-expected track conditions.
Stewards ordered Counter Punch be scoped to ensure the horse had not bled, but no signs were revealed.
His trainer Mark Oulaghan told stewards he was satisfied with the performance, given the track conditions.
No rain is forecast for the next three days in Christchurch, so significant rain late in the week will be needed to turn the Riccarton track into what Counter Punch and Mr Align need to produce their best.
A year ago, the first day of the Grand National meeting was similarly run on a reasonable surface, but heavy rain produced a greatly different track for the Grand National Steeplechase on the final day.
The official readings stop at a heavy 11, but in reality it was closer to a heavy 19 that day.
The favourite, Jack's Point, took 1:40.23 to win over 1400m and Blancpain required a snail-like 2:25.3 to win the 2000m Winter Classic.
Mr Align and Counter Punch would love a similar surface.
Karlos tried hard to pull Tobouggie Nights back in the closing 150m in the Koral after becoming unbalanced over the second-to-last fence.
Given it was only his third career steeplechase and, more importantly, his first this year, there is potential for considerable improvement.
He returned after Saturday's second with blood in a nostril, but a veterinary examination revealed it was a laceration, not a bleeding attack.
The additional distance will be no issue for Karlos - last September he finished only three lengths away in second place behind Hypnotize in the Great Northern at Ellerslie.
The ominous comment for the opposition came from winning rider Richard Eynon. "This bloke isn't entitled to be doing what he's doing. He doesn't know anything, but he keeps doing it.
"He draws to his fences beautifully."
Unsurprisingly, the credit goes to winning trainer John Wheeler, who was not at Riccarton on Saturday, but is much more likely to be there this week.
The distance of Wednesday's $57,500 Grand National Hurdles is potentially problematical for unbeaten hurdler Borrack.
The impressive emerging jumper has now won his past four straight, but to continue with Grand National victory would be something else. Grand National Hurdles are brutal races, particularly for front-running horses.
The distance - up 1000m from Saturday's 3200m of the Sydenham Hurdles, has found out more than a few.
Borrack, as he showed on Saturday, loves to sit on the speed and in each of his four winning runs has led from at least the last 1400m. To do that on Wednesday would be exceptional.
Borrack and Cody Singer never looked like being pulled back on Saturday, scoring easily from Vamoose and the favourite, Foremost.
They could well be the biggest dangers on Wednesday.
