I have a .45 scorpion with the 4.0 inch barrel and it has been having cycling issues.
I have had it since 2012 but with being deployed and training so much I haven't had enough time to try to fix the issue.

I reload and have had limited success but now it keeps failing to eject (new and reloaded ammo with different powder loads), the spent case will either not extract all the way or it will get caught on the round in the mag and the extractor will "let go" (best way i can think of putting it) of the case with it still half way in the chamber.
I tried a different mag but still didn't help.

Is this a problem with the older scorpions?  
Any advice would help...or should I start looking for a kimber lol

First try different magazines. Your description is a little confusing, maybe a feed issue? Does it work if you fire a single round with no magazine in it?

Like Chip McCormick or Wilson.

Then call Sig.

Ya sorry its hard to explain, so yes it dose fire with out fail but pretty much dose eject

I had issues with both stock mags.  Tried Wilson Combat mags and never another failure after that.

Use CMC mags. If not send it back to SIG

What bullet weight, powder and charge are you using.  Sounds like its weak ammo if its not ejecting.   My scorpion had issues feeding, 2012 vintage.  I had to polish the breechface, jhook, and chamfer the firing pin hole to get it to run right.

My scorpion carry would malfunction occasionally. The mag had lots of up and down play. I put in a different mag release and it made it 100 percent. David

Mine did the same thing but stopped after 100 rounds or so. No issues since then. I love mine.