I did see your NoFlash content. I'm not certain that all bots see the NoFlash exactly as you expect. For example, since googlebot does try to crawl flash it may not be seeing your noflash content. RogerBot is almost certainly not a good proxy for Googlebot on your site.
I suggest you log in to Google Webmaster Tools: http://www.google.com/webmasters/tools/ (validate your site if you need to)
Under the diagnostics tab, fetch your page as googlebot, then see if your links are being found.
You also do have a canonical problem on your site. http://www.myeyedr.com/index.aspx#/myeyedr-home and http://myeyedr.com/index.aspx#/myeyedr-home (w/ and w/o the www.) are two different pages in google and look like duplicate content. They are both competing with each other for links. I'd suggest you choose one or the other, and create a 301 redirect from the other. At the very least use a rel="canonical" tag on one version. http://www.google.com/support/webmasters/bin/answer.py?answer=139394
You can also specify only one version be indexed in Google Webmaster tools but it's better to solve it on your site, so it's resolved for all search engines.
The index.aspx page you mentioned is redirecting to the myeyedr-home page.
I would still suggest you rethink your flash home page. It simply doesn't have any content on it to signal Google that your are a relevant site to eye exams for example. Outside of your title tag, the keyword "eye exam" doesn't appear anywhere on the site. You have a bunch of keywords in the Meta Keyword field which isn't used by any search engine but does tell your competitors what you are trying to rank for.
Consider a little more content on your home page, with some good semantic markup H1 tags, etc... Alternatively, just don't try to get traffic to your home page, since it isn't designed to rank well. Instead create more keyword specific landing pages, i.e. make https://www.myeyedr.com/request-form.aspx your most compelling page to get clients to book an appointment and then focus your SEO efforts around getting that page to rank well for "Eye Exam".
I know it feels good to build/own a "cool" site, but if I took you into the usability lab and made you watch your prospects try to use your site, you'd likely be very disappointed. Many users will find your unconventional GUI difficult to navigate. To say nothing of users with special accessibility needs, technical issues with Flash, Javascript, etc.. It's particularly ironic for an eye doctors site to be inaccessible to the vision impaired.
At the very least I'd be watching my Google Analytics very carefully. See what percentage of your traffic has flash disabled and/or javascript disabled. Note your conversion rate and bounce rates of those segments vs. your other traffic.
I also happened to notice that your book appointment form is quite extensive. You didn't ask for any forms usability advice but ask yourself if you NEED all that information before the prospect is allowed to walk in your office? Perhaps you'd book more appointemnts with a much simpler form that feels less overwellming. Then you could hand customers an iPad in your waiting room to fill in all that other info.
Good luck!