I have modified all "flying_bolts" to "flying_missile" in itemkinds1.txt (This was the manual fix I tried, mentioned in the quote spoiler from my first post.)
I notice absolutely no difference whatsoever.
Here is a fraps I just took of me shooting with a white snowy background. After I double checked itemkinds1.txt to make sure all "flying_bolts" entries were changed to "flying_missile".
I suggest you turn quality to max and go full screen to see what I'm seeing when I shoot.
Does cRPG use finalboss_bolts, finalboss_arrows, and finalboss_bows by default? If so I can just change those files for you and get the native flying arrows if there's no other solution.
EDIT : Oh you use the heirloom pack that makes it easier. I'll post something soon.
For me, currently I haven't re-installed the heirloom pack after last patch, so it isn't activated right now. But activating it would just take a few minutes if I needed to. Willing to try anything, thanks!