EnderIO and Flans Mod are both asking for player.func_71045_bC and equipped.func_77973_b simultaneously, but look for different instanceof variables (IConduitControl vs. ItemGun). This is somehow causing EnderIO to overwrite the crouch+scroll function within Flans', causing the ItemGun to attempt to change its EnderIO Yeta Wrench mode, which it obviously doesn't have, instead of it's intended crouch+scroll function of initiating dual-wield.

It isn't just Shift+Scroll, as I have crouch remapped to LCONTROL and it still happens. Simply put, when I crouch+scroll with no Flans Mod single-handed guns or Yeta Wrenches in the hotbar, the hotbar scrolls as normal. When I have a Yeta Wrench in the hotbar, it scrolls as normal until I reach the wrench, then scrolls the wrench. When I have a Flans single-handed gun in my hotbar, it scrolls as normal until I reach the gun, then stops, with no visible action. When I changed the Yeta Wrench mode in the config file, crouch+scroll works as normal, scrolling the hotbar until reaching a Flans single-handed gun, then entering Dual-Wield mode.

If Shift+Scroll does anything when there is no Yeta-Wrench in the player's hand, that indeed would be a bug. So if you'd be so nice to describe what actually happens, so I don't have to hunt down Flan's, setup a new Minecraft installation, find out how those pistols work, and test it out just to see if there is a bug?