Please be verbose (pun intended, lol).
I'm not a GNU/Linux guru, but I've been using Ubuntu religiously for 6 months now. It usually helps people to know what you're working with. Like: What is the brand of your computer, what flavor of Ubuntu are you using (U/K/X/Lubuntu?), what version of Ubuntu are you using, and which version(s) of WINE do you have installed? Stuff like that. You know, help them to help you.
In the meantime, I can give you some recommendations.
You can install Runes of Magic on (?)buntu in two ways:
1.)
Buy the program "CrossOver" by CodeWeavers (the same developers who make WINE):
http://www.codeweavers.com/products/#cxlinux.
These guys offer
paid-support for WINE; more info here:
http://www.codeweavers.com/about/support_wine/. I highly recommend that you buy CrossOver for Ubuntu, and I'm sure it will help make installing Windows software easier and faster. Besides, all the money they get goes to further development of The WINE Project! (: I currently do not own a copy of CrossOver, but I plan to buy it this year. Gotta support our Open Source developers!
2.)
Install "Play On Linux" from the Ubuntu Software Center.
There are a few front-ends/GUI's for WINE that are good. There's
Qt-WINE and
Play On Linux (anyone correct me here if you know of another app), but Play On Linux (POL) will be the most user-friendly to use. I use POL, and it's a great application for WINE. I have not yet attempted to install Runes of Magic on my computer because I am currently using Ubuntu 12.04 BETA 1 (as of this writing), and I prefer not to install my favorite games on unstable systems. Fortunately, the official release comes out on April 26th.
POL gives you a concise list of categorized applications that you can install. The interface is easy to use as it slightly resembles the Software Center application for Linux Mint 12. POL has lots of Windows games that you can choose to install either downloading it from the web or off an installation CD (like World of Warcraft). Now, I
did see
Runes of Magic listed among the games that you can install,
but I have yet to try to install it when the official release of Ubuntu 12.04 "Precise Pangolin" comes out. Try it that way. POL should install RoM in a new Wine prefix so it doesn't use your old RoM prefix (correct me here if I'm wrong).
Again, I recommend buying CrossOver for Linux (they also have it for Mac users too) to install your Windows software on Ubuntu.

Anyways, just give it another go.