It is possible to import your own waypoints if you use Jepp Flitestar - I have done it; I also have a DA40-180 XL with G1000.
However, I understood it depended upon the version of s/w in the G1000 (although I guess yours is reasonably recent with SVT?)
I used 5 letters for the waypoints.
can you send me such a file, to see how the waypoints are described?