Aaaand I EMERGE from under the exam books I've hidden in for so long, finally giving JCS thread a good browse and seeing this.

The problem could be due to two things:
1. Tiles are 32x32 in size. An image with a height of 1000 will not work because 1000 isn't a multiple of 32. You could do what craccoboy suggested, make it 992 or 1024 tiles high.

2. JCS can read BMP and/or PCX files, but there is a condition to that. The image will have to be 256 colours with its own palette. It will not read images with any more colours, JJ2 is an old game and still uses the ancient '256 colours' as a base. It's a pain, but thats what we get.
This could be the reason you are having problems with your other sets aswell, paint programs like photoshop and paint shop pro are far too eager to save somehting in as many colours as possible. Hey, it looks better, so why not do it?

Apart from that, can you tell me what the exact error is that JCS gives you when it cant build the tileset/s? I'm pretty sure ive seen all of them (including the weird one 'Too many colours in palette') and it'll tell me exactly what the problem is.

*hopes its not too late for a reply*