You are comparing a Xeon 5698 processor (4.4 GHz) with an E3-1265 (2.5-3.5 GHz). Here are some reasons why they measured the single thread E3 performance as faster:
- L1 caches are twice as big on the E3.
- L2 cache is twice as big on the E3.
- More register read ports on the E3.
- Better branch predictor on the E3.
- Instructions are cached after decoding on the E3.
The Xeon processor you are comparing is two families older than than the E3-1265. See this for details on how the Ivy Bridge family is faster than the Nehalem family.
(Note that it is hard to tell what exactly is causing the difference without knowing exactly what the benchmark code does.)