Yes, the values will be different. Cufflinks calculates statistics based on a single BAM input (sample, replicate) where Cuffdiff utilizes two or more.
The details are included here (summary) and in the linked publication (full algorithm): http://cole-trapnell-lab.github.io/cufflinks/getting_started/#common-uses-of-the-cufflinks-package
Related Q&A: https://biostar.usegalaxy.org/p/4683/#23418
Hope that helps! Jen, Galaxy team