No problems here with such a link (oS 11.1).

data:text/html,<a href="http://mail.hillbarn.plus.com/testing-area/Ellso_Maintenance/Ellso_Maintenance.jnlp">Link</a>

Start Firefox in Diagnose Firefox issues using Troubleshoot Mode to check if one of your add-ons is causing your problem (switch to the DEFAULT theme: Tools > Add-ons > Themes).
See Troubleshoot extensions, themes and hardware acceleration issues to solve common Firefox problems and Troubleshoot issues with plugins like Flash or Java to fix common Firefox problems

If it does work in Safe-mode then disable all your extensions and then try to find which is causing it by enabling one at a time until the problem reappears.
You can use "Disable all add-ons" on the Safe mode start window to disable all extensions.
You have to close and restart Firefox after each change via "File > Exit" (Mac: "Firefox > Quit"; Linux: "File > Quit")

I have the same problem.

I am running 3.6.13 (on 32-bit XP); I started in Safe Mode, and switched to the DEFAULT theme.

Here's my use-case: I have a server whose domain name stupidly includes the letter "L", which is hard for people to distinguish from a "1" when it's lower case. For easy copy and pasting, I want to keep it like

 http://X1234L.foo.com/server/path

not like

  http://x1234l.foo.com/server/path

which is how Firefox keeps changing it.

- rob

Something like this?

javascript:(function(){var up=location.protocol+'//',ud=location.hostname.replace(/^[^.]*/,function(r){return(r.toUpperCase())}),un=location.pathname,us=location.search,uh=location.hash,url=up+ud+un+us+uh;void(prompt(url,url));})();

I have a similar issue in that I need to type capital letters in a login name and Firefox keeps changing it to lower case. Since the login is case sensitive, I cannot login using Firefox. I'm running Ubuntu 11.04 with Firefox 5.0.

This is quite annoying!

Make sure that you haven't saved Uppercase and Lowercase versions of that name and password.

Remove saved Password(s):

• Edit > Preferences > Security: Passwords: "Saved Passwords" > "Show Passwords"