So when the songs plays through FL Studio the quality is fantastic, but then when I export it into a WAV or MP3 some instruments keeps quieter than others when playing at the same time and the bass muffles a lot of instruments, but in FL Studio itself it sounds professionally done. So is it a rendering problem? or can anyone help?

It could be the Resampling setting. Make sure it is the same as what is set under Audio Options.

If that was not the problem, it could be one of the synths oversampling settings. Make sure they are the same again, for both render and draft quality.

What are you exporting? MP3 will do that. Make sure you have it set for 320kbps sample rate and there's the sinc interpolation (look that up in the manual)
Also, if you play a song in FL with ASIO, and then play your wave or mp3 in a media player by just using your default soundcard, it will sound different. I think people say it's not supposed to, but it does.
When I was making synths with SE, I'd do presets in VSTHost which ran off main soundcard, but when I'd do them in FL (ASIO), the sound was much brighter.

Very doubtful, it is very hard to tell the difference between wav and mp3. Not many people can.

Most probably your sample rate setting.

There are enough people who can hear the quality loss of a 128 kbps mp3, especially on monitors. And if he can and it bothers him, why should he care about all the others that don't.

Oh I can definitely hear a difference between wave and mp3. Are you kidding?
I streamed waves and the converted them to mp3. Bass gets mushy, highs get higher.
I think that's a problem especially with younger people who have been listening to mp3s and AAC formats through little tiny bud headphones all their lives...
(my geriatric rant)

Make sure there is no additional oversampling on anything, interpolation should be the same as live, disable HQ for all plugins, make sure any instances of plugins like Sytrus have the quality set the same for playback and export. Weirdly enough you really get worse results by exporting at higher quality than what was being used for playback, it changes the makeup of the mix a lot, before I figured this out sometimes I would wind up having to export a song in excess of 20 times trying to tweak things that were appearing in the final wav that didn't appear in FL...

Yes there's that oversampling thing also. I'd made a comment on how 'smooth' Z3ta 1.5 sounded compared to v2. Well, 1.5 was set to 1x oversampling. V2.1 was set to maximum oversampling. Sometimes the sound difference was startling.

Here's the example: http://www.youtube.com/watch?feature=player_embedded&v=7FE66 AoituA

you can hear the intro bells quiet down when the DX7 E.Piano starts playing, and the bass quiets down other instruments. I did all the mixing and mastering in FL Studio, and it sounds great in the program, when it's exported it starts sound like this. No matter what setting I put it on, my resampling is the same as in the program itself... so I don't know what to do.