I've yet to see posts about this problem on any site but am hoping someone will know what I'm talking about here.

When firing an automatic weapon, when the clip/magazine/whateverthefuck runs out, the animation continues.

So I look like I'm jack hammering the air until I let go of the mouse button.

I'm assuming this is an issue with either Manual Reload (http://www.nexusmods.com/newvegas/mods/37090/?), Improved Automatic Ironsights Animations (http://www.nexusmods.com/newvegas/mods/48509/?), or the two together. However there seems to be no comments on either mod about this issue. So I'm posting this here both because I want help, and because this seems to be a far better community.

Thanks in advance for the help, thanks for reading this far regardless.

I believe it is a problem with manual reloading, I had this issue before and i turned off automatic reloading with MCM in the NVEC settings. 
EDIT: yes it is an issue with the manual reload mod, i suggest removing it entirely..

Thank You. That's highly unfortunate though. I wonder if there is any chance for a fix.

I just decided to turn on automatic reloading again in the MCM menu with NVEC and it's working for me now. Maybe you might have some luck with NVEC or it's just certain weapons that work properly. If you do decide to download NVEC note that it is a big mod (and to download) and might conflict and or override many of your other mods.

I have NVEC bugfixes and CTD but manual reload doesn't show up in MCM for me and the problem has definitely persisted. Does the MCM extras module add manual reload to MCM? I feel like I'm missing something blaring.

Maybe your font is too big, it happened to me when I didn't use DarnUI because the option was literally off-screen/menu. The option should be called Automatic Reload and it is in the main NVEC settings near the bottom I'm pretty sure.

Already using Darnified. I just don't use the full NVEC, I use the two separate bits because I don't want the enhanced content stuff.

I think Manual reload is only included in the Complete Version of NVEC (not 100% sure so don't quote me on that).

I've used both the separate Manual reload as well as the manual reload included in NVEC Complete and haven't ever experienced this issue, however, I have had a similar issue using JIP select fire and switching a weapon rate of fire to burst. While this only happened when I used 'tgm" in the console (i do this sometimes to test out new weapons without having to waste a lot of ammo...I try not use console commands to get more and I always forget to craft more ). If I haven't used god mode then burst fire works normally.

I'm not sure if your using that mod or using god mode but that's the only thing I can think of that could be the reason for it.

I went and did a few tests with things and the issue is occurring with all automatic weapons, modded or not. I tried toggling god and demigod modes on and off to no effect. I do not use JIP select fire. I'm going to try a reinstall of manual reload and hope that helps. Any other suggestions would be much appreciated.