The Blues' 26-12 win over local rivals the Dragons came three days after their cruel dismissal from the Heineken Cup in a penalty shoot-out in last weekend's semi-final.
Shanklin scored a first-half interception try to lead the march to victory.
But the 29-year-old suffered further heartbreak after Sunday's defeat by the Leicester Tigers as he popped his shoulder in a tackle late in the game.
The shoulder went back into place almost immediately, but Shanklin now faces an agonising wait to see what the doctors have to say about his chances of making a second tour with the British & Irish Lions later this month. He went straight off to hospital after the game for X-Rays.
Head Coach Ian McGeechan has already lost Munster scrum half Tomos O'Leary from his original 37 man squad, the Irish international suffering a broken leg against the Scarlets three days after being selected, and now Shanklin has joined the pre-tour injury list.
There is also a disciplinary case hanging over Munster back row man Alan Quinlan for alleged eye gouging in last weekend's Heineken Cup semi-final against Leinster that could see him ruled out if he receives the minimum recommended ban of 12 weeks if his citing is upheld.