Are you using your own customized settings in IE's general tab "font", "color", or accessibility sections (buttons)?
Keep in mind that some sites can control this and may have chosen to override or not show them. This may be planned and site should be considered suspicious or in the least user unfriendly. Another possibility is poorly scripted/color choices for the site owner.
If not the above how about the below:
>"underline links" setting:
Make sure it is set to "always" http://malektips.com/internet-explor...derlining.html
There is another setting that may help and it is called hoover color. This is enabled via IE's tools>options>general>colors button. Make sure windows colors is checked and if you want live links to show up in a different color when you hover the mouse over them click enable hoover color. Personally I don't use this but it is an option and a user preference.
If this is just a few sites it may help to see them if you right click and "select all" to highlight everything on the page. Any seemingly invisible buttons should show up.
Make sure IE's view setting is set to allow the "status" view. This will reflect text and urls at the bottom left of IE page.
If using IE 8 and again this is random or only effecting a site or two you may need to use "compatibility view": http://www.microsoft.com/windows/int...es/easier.aspx
Via IE's tools>compatibility view is an option that will be available.