I took Both B'Tran and B'Tran VA Missions to Explore 3 Systems in each section.
I entered B'Tran the first time under the VA link. I proceeded to do 3 Explore missions, and the checked the Starfleet list to get the credits and move on to the regular B'Tran sector. There were no check Marks along side the Commander who gave me the missions. I then checked my Mission list, and saw that there were indeed 2 B'Tran Listings, so I exited B'Tran and re-entered under the VA Link again, and did 2 more missions. Both of the B'Tran mission listing showed 0/3 missions complete. I had just completed at least 5 mission in total.
I then exited the sector, and re-entered under the plain B'Tran link. After I did my first mission there, I looked at the mission list, and BOTH B'Tran listings showed 1/3 missions complete. After completing the second mission, the listing showed 2/3.
Doing B'Tran missions on the VA Link does not give credit for them, but doing missions on the NON VA link gives credit to BOTH B'Tran Sector missions. Serious Glitch in the Programming Links Me Thinks??