Can't compile things to check
Library file changes
Are you using a library like the bcm2835 IO library by Mike McCauley? If so have you updated the library since last working on this project and need to copy the new header file into your project source?
Can't run things to check
Using eclipse and putty
Delete the old .a file off the RPi. Even though putty may appear to be uploading the new executible file, it sometimes need the old one to be deleted before it will work.