For me, just watch it for a bit. Here's one I saved when it was showing a clearly wrong count, but on reload it shows the correct count and doesn't show a wrong one until I watch for a while, is there any way to set a script to compare what's being displayed with the circuit value and what's on the segment(s)?
Your first image shows some item hidden under the top inserter.
But in the provided savegame the top belt is in pulse mode, while the bottom is in hold mode, but when I run the save I can't see any problem. The network shows 2 items when the 2 items stay on the the bottom belt in hold mode and that is correct.
In the second savegame, both belts are in hold mode, and when I load it I can see the 2 items in the circuit network, which is again correct.
Keep in mind that each belt piece behaves independently and has it's own settings.
Aggggh, _sorry_ </kowtow></begforgiveness>. It is as you say, items hiding in shadows+clutter, hasty testcase setup, general inattention to detail on my part. (/me hangs head)