Well, A lot of people have been facing similar set of issues with skins so I thought I would list down some of the common problems faced by skin designers and skin users alike and their solutions. I hope some of the skin Gurus in this forum (and there're plenty of them) will add to this list so that future skin masters find it easy. This can be one place to list all skin-related issues (since it is quite tough to search in the forums.... )
Crap over, here it is:

1.Problem: Java Games/Apps dont work on some/all skins.
Symptom: On running a Java App, it gives application error. The error may not occur on selecting a different skin.
Analysis: There is always one skin which has to be the full skin (it has all the image files in it). (For eg. for XYPACK is Xymoto). When a light/incomplete skin is loaded, the phone software takes the missing icons from this skin, or if an erronous skin is selected, the phone loads this default skin. If you happen to delete this skin accidently, you will experience Java errors.
Solution: Open the skin with whichn you are facing Java problems in Skinner4moto, untick the 'Light skin' option and save the skin. Now install this skin with SkinManager. The skin will now work fine.

2. Problem: Home icons dont work.
Symptoms: On moving the joystick up/down/left/right at home screen, the icon appears but nothing happens.
Analysis: The home screen icons need to be animated (have atleast 2 frames in the GIF file) for them to work. This problem suggests that the home screen icons have not been animated.
Solution:Animate the icons using any animation tool (like ULead GIF Animator freeware utility). If you're not sure how to go about it, I suggest you read my guide's ANIMATING THE IMAGES section.

3. Problem: My menu appears jumbled/ Phone hangs while navigating main menu
Solution: You are facing a mma_ucp issue. Read this GUIDE.

4. Problem: While typing messages, the characters appear overlapped/ messy.
Solution: You have set the skin transparency factor to 0. Open the skin using skinner4moto, and change the transparency percentage value.

5. Problem: I changed the skin, but some icons like Video Camera and iTunes dont change.
Analysis: Certain icons are not a part of the skin. These include all battery and signal icons, iTunes icon, Video Camera icon, etc. To change this, you need to flash with a different DRM.

Please post any questions, problems, issues related to skins in this thread so that some of the experienced skinners can solve these (and I can continuosly update the issues list with the solutions).

Hope this is helpful in some way.