Is the plastic loading tap lever in perfect condition and completely tight? We tend to think of pellet clipping as being a side-to-side issue, but if the tap lever has any play at all then you can get variation in tap closure which will cause up-down clipping.

As you say, clipping would be more likely to cause inaccuracy with every shot, but this is only true of lateral clipping. Variations in tap closure could be much more random. Shoot pellets into a rolled up towel at twenty yards and examine them, you'll soon find out if they're clipping.