Lighting...

I'm using a home made light box, with a florescent light bulb above, shining through a small cut hole in the ceiling of the light box. I mainly use this for Macro shots...

The florescent bulb is white, not a yellow, so my picture have a nice white background...

My camera seems to not want to notice it is white... My camera literally turns the background and surrounding light areas yellow... But with my flash on, my camera now sees the background and surrounding areas as white...

Example

YELLOW: No Flash enabled.
http://i50.tinypic.com​/2h3dlj6.jpg

WHITE: Flash enabled.
http://i45.tinypic.com​/1se3kl.jpg
Please excuse the grey in the background, I am going to edit that out with Photoshop...
Also in the second picture excuse the shadow, My camera was too close to the bottom of the box.

Is there any reason why my camera does this?
It is a Nikon Coolpix L100, Sadly it doesn't have an option to edit the ISO... But it's a camera for a beginner.

You need to read up on how to color balance your camera properly. Do you have a manual? If not, just google this. It's actually easy to figure out once you do a little reading. Your camera's settings are wrong for the setup that you have but I dunno how to color balance it as I never used that model.

The White Balance should be set for Florescent light. Check the manual for how to do that.

Like Sue said, the right White Balance is the key, artificial lights can throw things off. If you have an appropriate WB setting for the flourescent light you should try it out, but do not leave it on that setting for the flash -- either use the Flash setting or Auto (likely what you've been using).

It may be useful for you do do some research on lighting for this project -- there are lights available with known "color temperatures" that can be more suitable for this type of thing and can work more closely with a flash temperature so that you don't have to switch back and forth. I don't have any details on hand, but I've read about them on the InterWebs! Check the Flash/Lighting section here -- someone may have some suggestions.