A couple of things to check. First, you are ensuring the theme is checked in Winterboard (and that you've respring the iPad)? Then, is the them above all the other checked themes in Winterboard? Winterboard has a hierarchal system in that the topmost checked theme will take precedence over the others.
If all those are okay, then you may just have a theme that is not compatible with your iPad version or loaded iOS (or both). Apple changes the names of elements in every iOS and the names are also different depending on whether your define is an iPad 1, 2 or 3. Then, while some tweaks work on all devices, some are iPhone only. For themes especially (that don't change the file system - they just create an overlay) - the name of something is very important.
Hopefully, some of this is of value and helps.
Marilyn