At the heart of the M3 is still the inertial system so it certainly can affect it. That said, I've found it to be MUCH more critical of having a firm shoulder mount than anything else. If I "free hand" where I let it swing freely my M3 or SBE's, they will fire and eject the empty. But, because they don't have any real resistance, they don't go back far enough to hit the cartridge release and thus never picks up the next cartridge.
So, back to your question, you can overcome this issue of lack of resistance (in my case) or extra weight added (in your case) by shooting a higher DRAM-EQ shell. For the 3.5" capable SBE's, I end up shooting the 1 1/8 oz load and it has solved all short cycling issues on both guns. They are still available as el-cheapo loads from Wal-Mart.