And while Jones himself struggled with his injury and rehabilitation, the Scarlets struggled with their form on the pitch.
Nigel Davies' men finished next-to-bottom after recording just three more league wins after Jones played his last game of the campaign in late October.
The 30-year-old has now been forced to have an operation to attempt to cure the problem that also saw him miss Wales' entire 2010 Six Nations campaign after featuring in every Six Nations fixture a year earlier.
It is the second time Jones has had surgery on this particular injury, with his AC joint having failed to rehabilitate fully in terms of power and strength at the end of last season.
Jones has not been the most fortunate when it comes to shoulder problems, having already had a shoulder reconstruction in the summer of 2006.
But while he is naturally disappointed not to be pressing his international claims on Wales' summer tour to New Zealand, Jones believes the timing of the surgery will give him the best possible chance of helping the Scarlets' turn around their fortunes next season.
"Obviously it is really frustrating for me that I'm going to be out for a bit longer," said Jones, who has played a total of 70 Magners League games for the Scarlets.
"But there was no real option for me but to have this second operation to make sure the shoulder is fully stable and to ensure I come back to full strength long-term.
"It's been disappointing of course to have picked this injury up when things were going so well but the region has been great and really supportive to me and I will be repaying that back on the field when I return.
"To have it done in the off-season meant that I would miss the shortest amount of playing time next season.
"I've got all the motivation I need to get back to fitness as soon as I can with the World Cup coming up and just look forward to playing back with the Scarlets boys again.
"Hopefully by doing well for the Scarlets, I'll be back for Wales as well."
Jones is expected to be sidelined for four months, meaning he should return in time for the Scarlets' opening Heineken Cup fixtures in October and Wales' autumn internationals a month later.
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