Are you sure you're using the absolute newest version of my miner? mtrlt's 0.5% speed increase accidentally had a bug that would cause similar behavior to half of shares missing. I fixed it shortly afterwards.
A dead giveaway of the bug is using -dd and seeing a ton of hardware check errors.
Interesting, last one I pulled down was yesterday. I'll try that flag and see if hw errors pop - I assumed that they would show up by default.