I can't answer your question as to why, but I found a way around it. If you enter it as 50 @ 100 (base 10) as Rocket J Squirrel suggested to get the correct total of $50,000, you can then go to the transaction list and edit it. During the edit the "(Base 10)" next to the price box disappears and Quicken will let you enter, e.g., 50 bonds at $1,000 each or 500 at $100 each if you want.
