Was this a situation where your L2 was indexing OK then suddenly stopped? Or did you change something (like swapping the barrel to another caliber)?
Asking because I just experienced a similar situation when I swapped the 0.25 and 0.177 barrels between my two L2's. The action that originally held the 0.25 barrel/mag indexed it perfectly but would not fully index two or three times per magazine with the 0.177 setup. I checked the barrel alignment and the other things you mentioned...turns out the issue was the grub screw that adjust the resistance on the rod that extends from the magazine into the action.
In my case, the newer 0.177 magazines are now plastic and not aluminum like the earlier batches so they're lighter than the older magazines. Apparently this affects how they index so on every 3rd or 4th shot with the 0.177 magazine, it would not fully rotate to the next slot. It would rotate MOST of the way, but when you fire the next shot, the pellet wasn't fully aligned with the barrel so it would misfire and jam the pellet against the end of the barrel.
What I had to do was lessen the resistance that the grub screw was putting on the magazine rod and that resolved it. To do this, there is a silver ring just in front of the magazine that has two set/grub screws in it - one on top for the tension adjustment and one on the left side that locks down the adjustment screw. First, loosen the one on the left, which will allow you to turn the adjustment screw. I backed that top grub screw out several turns, then tightened the set screw on the left to hold the top screw in place and it's indexing fine now.
Hope this helps; I'll take and post a picture of the screws in question when I get in front of my L2 tonight.
BTW, I can't take credit for solving this - it was yet another instance where @jack.k helped me out...
Edit: adding pic below
Loosen the set screw on the left (blue arrow), back out the top set screw on top (green arrow) to lessen resistance on magazine rod and then retighten screw on left side to lock down the top adjustment screw.