We started with R2009, and I found this issue right off.
Our reseller told us to stick with it and it'll work.
Then, supposedly, R2013 was going to be the magic fix.
Meanwhile we just get the run-around.
I still don't see how this is supposed to work.
We also use a single bank account in one corporation to pay checks for all of the corporations A/P invoices. Currently, again, automatically, behind the scenes, our accounting package does all the intercompany entries to AP and Cash to make this work. In NAV, AP payment seems below basic capability, I really don't see how it's going to deal with this without a lot of constant intervention and journal entries on our part. I am seriously, seriously underwhelmed by NAV and seriously mad at the sales job used to get us to sign up for this.