So, as you may know, I'm making the blaze trooper. I wasn't having any major problems, until I decided to try to merge two parts of it. Just two objects. This is what I get:
Original:

Merged:

Why did this happen? I merged two objects. Can this happen if they share a texture?

To merge the materials and UVs after merging in Mod Tool(Mod Tool Layout):
Open an Explorer(8 key)
Then click on "Show Tree"
Find the new "polymsh" object created from the merge and expand it
Then expand "Polygon Mesh" and you should see the "Merge Meshes" operator
Click on it to open the ppg
Lower the Tolerance to zero or .001 if some objects should be connected
Press the "Merge" button in the "Merge Properties" section under "Materials,UVs,Vertex Colors,Weight Maps"
Hide or Delete the inputs if you want to, then close the ppg.

You would probably be better off switching to XSI Default(Pro Mode), you can go to "Modes" in the top toolbar to change it.

Well, the thing is, my problem isn't the UVs. It's the actual poly mesh. It's messed up. Thanks for that info, I did need to know how to do that, hehe... Now I can mshex all of my objects. Maybe.

Well, you never specified which problem you were having with "merging", and according to the second pic you obviously didn't merge the materials/UVs or lower the tolerance, try to be more clear when you post topics and explain what the exact problem is that you're having, this helps us help you.

hehe... sorry. Wait, if you're referring to the fact that most of it's untextered, well, I haven't hidden the original in that pic.

Hiding the original is irrelevant, the torso/legs/arms/hands/head/feet of your merged character in the second pic haven't had their UVs/materials transferred yet, that is what I was referring to.

Well, my problem was the fact that the polymesh that I get from the merge is all messed up. So, are you saying that merging the UVs will fix the polymesh?

No, the polymsh would be fixed by lowering the tolerance.
If you don't understand how merging works then press F1 and have a look in the XSI docs.

Edit
http://softimage.wiki.avid.com/xsidocs/property8017.htm

Small question in between;

In XSI 6 the option is there to merge weights to, for some reason my checking-box is light-gray there meaning i can't do it (in 5.11) Is there a way to fix it? So both objects are enveloped, to bones, but still this option isn't available..

Foundation can't merge envelope weights because the GATOR operator is disabled, and merging envelope weights is one of the better features of GATOR.
Mod Tool has GATOR, MOTOR, Polygon Reduction and RBD just like Essentials, but it has some other limitations like:

• Watermark
• Mod Tool supports only DXFX and CGFX material types. Mental ray materials are not supported.
• Mod Tool supports only polygonal mesh primitives.
• Exported geometry is limited to 64000 triangles.
• The mental ray renderer is used only for Rendermap and Ultimapper. All other mental ray rendering is disabled.
• Maximum resolution for Ultimapper maps is 512x512.
• Images output using the hardware renderer are limited to a maximum resolution of 512x512.
• File>Merge is disabled
• File>Export>Model is disabled

So there's no way to install GATOR? It does display it, only it's not usable..

Thanks for the info Ace