Let's start with the fundamental interaction style: go to a site in IE with a two button mouse, and right click an HTML link. Open, Open in New Window, Save Target As, Print Target, Copy Shortcut, Add to Favorites, ... Translate into English, whatever, depending on what software you have installed. Most aren't used that often, but "Open in New Window," I use that a LOT. That's a very concrete example of how your examples "could" (in fact ARE) annoying.
Okay, another example of standard interaction, say I want to find the support link on a busy site with a lot of text. I usually <ctrl-f>support<return>. If there's an HTML link on the page called support, it scrolls the page until it's visible, then highlights the text. If it's flash navigation, it would pop up a box saying to "not found."
Another example, say I'm working on my Sony laptop with a 5" screen, and having trouble reading the text. In a standard web site, I hit the control key, scroll my mouse wheel downward, and all the text on a page gets bigger. With flash, it doesn't. These last two examples apply to graphical navigation systems too, but I typically find those more annoying than text, and flash more annoying than graphics.
Then there are the varying versions of Flash...my laptop had an older version of Flash until recently, as it uses a slower modem to connect, and nav bars written for one version of Flash don't always work for others. The only example I can think of was internet-expo.com's site, because that's what I was trying to navigate in Vegas, and it just wouldn't work for whatever reason. You'd hover a mouse over the menu, and nothing happened. After a flash upgrade and system reboot it worked, but there's another example where it's just plain annoying.