I'm the same. Top order batsmen (1-3) yet I've only had one score of 50+ (64*) and the rest have been 35 or under this season. This season has been the most confident I've felt batting (apart from today's game where I just couldn't hit it off the square, first single figure score for 6 matches), yet I have almost nothing to show for my best season. I'm the highest run scorer in the 3's, yet haven't had the opportunity to move into the 2's, which even if I did, I would be down the order, so thats annoying.
One thing I've found this year is to just take my time as the runs will accumulate. The longer I'm batting for, the more likely it is that I'm going to get runs. Unfortunately there's always going to be someone who can just hit runs much faster than I do. Just don't rush if things aren't going your way.