I'm pretty sure that's not a VA issue.
Those tabs are addressed by the Q and E keys and there's no way for the profile to know what tab you left off at (unless you structure some commands to do so), so when it opens (I'm pretty sure) it assumes you're at the Navigation tab and then tabs over 2 to Contacts, for example. However, if you close the panel while you're at the Contacts tab, the next time you say "Contacts" you'll find yourself at the Inventory tab, because the profile thinks it's starting at the Navigation tab and goes over 2 tabs.
I solved this by sending the panel back to the first tab (be it the Target or System panel) when closing.
I ran into a multitude of other issues that i've solved, one-by-one. For example, when you open either of the maps, Galaxy or System, it auto-closes the panels. If, again, you're not at the first tab, you will get odd behavior when you open the panel again.
You'll also run into issues if either of the panels is open and you: got to/drop out of hyperspace or supercruise (just before the jump or the drop, the panels will close...at least they do for me), if you open the Comms panel..etc.
I think I've solved all the instances where the panel tab location can get screwed up, but that ended up making the panel commands my longest ones, in a relative sense. I can go directly to any tab when the panels are closed without issue...so far.
Anyway, I hope I didn't misunderstand your issue. But it sounds exactly what I thought when I first starting using VA with ED and used a pre-made profile.