Frustrating. Which version of Vara are you using? Free or licensed?
Are you within clear line of site of an FM node to link your tx'n?
Fresnel effect can be a problem if it is a long hop with obstructions along the path. Tall buildings especially.
If those things check out ok, make sure to override anything D-Star on the ID5100. If its built-in digital encoding/addressing bumps into the VARA data stream the signal will be messed up for sure.
We are experimenting with the same set-up as yours with an ARES installation here. The ID5100 is a sophisticated radio and D-Star is complex itself. Fellows with a neighboring club who bought into it on initial release found it cumbersome for portable/mobile emergency operation and gave up on it. We ran an exercise with ours last year and even our most advanced operator found the ID51 a challenge to use. So we are wary. Please let me know how it goes, or doesn't.
Good luck.
Al
VE3VTT