Philippaerts's team-mate Josh Coppins was a solid third when he stalled the bike on a jump and eventually dropped down to fourth, ahead of Kawasaki's Estonian rider Tanel Leok. Marc de Reuver was disqualified as he started outside of his gate position.
All of which means that round one winner de Dycker still holds the red plate, now by seven points over Ramon. Philippaerts has moved up to third ahead of team-mate Coppins, while CAS Honda's Billy Mackenzie has slipped down to fifth after finishing eighth at Bellpuig on Sunday.
"It was very difficult and on every lap, on every obstacle, you had to concentrate hard because the track was always changing and the mud and water was hiding the bumps and ruts," said de Dycker. "I'm still leading the championship by seven points which I am very happy about. I've never led the series before and to be leading for two rounds in a row is really good for me."
The MX2 class almost got two complete races, the first of which was won by championship leader Tyla Rattray with a dominant gate to flag performance. A solid Steven Frossard was a comfortable second until he had a problem with his brakes, dropping down to twelfth.
Reigning world champion Antonio Cairoli took an eventual second place after a difficult start, as he was in the middle of the pack through the 'swimming pool' that was turn one. Guarneri ended up an unexpected third in moto one - despite being doubtful for the grand prix after sustaining a broken ligament in his right collarbone.
Guarneri continued to defy his injury in moto two and soon found himself in the lead - after Tommy Searle had aquaplane out of the holeshot at turn one, with his successor Nicolas Aubin falling soon after.
Despite the worsening track conditions - by now riders were literally queuing up at the bottom of the steep hill while they waited for fallen rivals to move aside - Guarneri kept up a decent pace and was handed victory one lap early when the red flags were finally waved.