I posed this question on here a couple of weeks ago, more due to my curiosity. The consensus from the few responses I received were ambivalent towards it and I got the impression that people neither knew or cared. Which surprised me, because it is important if only to reduce premature wear, which your experience shows will occur.
I have since checked out Sheldon Brown, who suggests that a double requires a chainline of circa 43.5mm, whereas a triple is best set between 47.5 to 50mm.
How many spacers do have have on the DS crank? Possibly 2, each of which are 2.5mm. Try removing one first and check the chainline, although it will always be ‘off’ with the big ring to bigger cogs or vice versa, but you’re just looking to ease the situation. If you want, you can remove the other one and check that. 1mm metal shims are available, if you feel that does too much.
Hope that helps