Some links for you :
Software : Try Deep Sky Stacker. It's freeware and designed for astrography. The site has some useful tips on technique and method as well, so read those even if you don't use the software.
General purpose software :
I do use Darktable for general photography processing, but it's not designed for astrography. For very tough RAW ...
There is no way I can imagine that the same jpg can one day be 'clean' & another day be 'grainy', then the next back to 'clean', unless it is being viewed by an app that is failing to correctly load it, or is re-interpreting at load.
The file itself is either good or it is broken. Broken files don't demonstrate 'grain' they either show large blocks of ...
I believe ISO 2000 is a bit high. I'd experiment with lower ISO, like 800. This is a good article explaining ISO in astrophoto.
Also, 2.5 secs per picture is a bit low for an object like that. That's why you only get the bright core, but no arms.
Can you expose more time, like 15 secs or more?
Taking more frames will help you to increase signal-to-noise ...