When you say half the scripts are just printed on the page, is it the same script called multiple times or different scripts? Is it always the same scripts that don't work?

If you're seeing the perl code, that means your server knows enough to include them, so SSI is working. If SSI was broken you'd see an empty spot where the include portion normally goes.

It sounds like whatever mechanism tells your server when to interpret something as perl isn't kicking in. So concentrate on that. Does it key off the file name? Something in the file? Can you replace the includes that don't work with one that does? Try replacing the ones that don't work with a "hello world" script. The point is to reduce the complexity until you can see what's different between the ones that work and the ones that don't.