When I cut my mat boards, the bevelled edge shows up a different colour (usually a grubby colour which clashes with the white or gray board surface), and I really dislike it. Are there any options?
The least expensive paper mats have a cream colored or off white core. Paper mat board is often buffered to help shift it from acidic to alkaline but this is temporary. They typically will return to being acidic and harmful for the artwork in about 5 years. Most of your inexpensive pre-framed artwork in department stores will use this type of mat.
You can also get paper mat that has a white core or a black core. White core will be closer to the white mat color but seldom match exactly. It will actually have even more contrast with a gray mat which may be advantageous since it will help outline the image. White core papermat is still recommended for decorative framing as opposed to conservative picture framing.
Your higher end rag mats such as Bainbridge Alpharag mat board and the Crecent Musuem Rag mat board are layers of died cotton all the way through, with no laminate. As others have mentioned they are the same color all the way through the mat and on both sides. They are also the most archival matboard and safest for your artwork.
A less expensive Rag board will have a laminate on the surface to provide the color. These are still very archival since the cotton is touching the print and acting as a barrier between the artwork and the laminate surface paper and the dies used for the color. These mat boards will have a white or black core that will usually not match the surface color.
Lower cost, but still very archival is alpha cellulose mat such as Bainbridge Alphamat. More pure than the paper mat but less expensive than the cotton rag. It will also typically have a white, black or gray core and then a surface laminate to provide the mat color.
This picture has some examples of different types of mat core colors:
http://www.framedestination.com/graphics/L_wood_frame_205.jpg
The top mat is Taupe (light brown) with a white core. Although the bevel does not match the core, it is a clean white look and provides separation between the Taupe mat and the gray middle mat. The middle mat is Ash with a grey core. We used grey core because we did not need another white line making the matting look too busy. The grey core is not exactly the same color as the Ash colored surface but it is close enough. The bottom mat is Almond with a white core. Since the photo image has a white border the white bevel of the bottom mat just blends in with it so you dont notice it. If the bottom mat had a cream colored bevel then it would just look dirty next to the white paper of the photo.
This picture is one of mine that I specifically choose to use a mat with different color core:
http://www.framedestination.com/graphics/L_metal_frame_117_silver.jpg
This was matted with an ivory black mat with a white core. Because this image is so low key a black mat would just blend in with it too much. This mat is available in white core or black core but I choose the white core to create the separation between the image and the mat. Again this is a Bainbridge alphamat with a clean white core instead of cream colored core which would look dirty and cheap.
There are no right answers, just lots of choices. Hopefully with the extra knowledge, and perhaps a little experimentation you can determine what works for your personal taste, your photographic style, and of course your budget.