Downloads not including transactions

It looks to me like Fauquier Bank uses Direct Connect as the method of downloading while Virginia Nation Bank uses Express Web Connect, which is more prone to problems, so my first thought is that those missing transactions simply aren't being picked up for some reason in the OFX files sent from Virginia Nation Bank.

You should be able to confirm this by searching in the OFX file (Help > Log Files > OFX Log) to see if that's the case.  OFX logs can be difficult to parse but in you know the dollar amount of the missing transactions and the dollar amount of some transactions that did come down immediately before or after one of the missing transactions, then looking for the dollar amount of one of the transactions that did come down should get you "close" to where that missing transaction should have been reported.  Scrolling up and down from that point should help confirm that the missing transaction simply wasn't included.

(The OFX log opens as a text file so using the "Find" function in Notepad should make the search process relatively easy.)

You could also search for the "missing" dollar amounts and if you find them in the file that indicates some other problem.

If the missing transactions really haven't been included in the OFX log then a call to Quicken Support

will probably be necessary.