First off, you should take a look at Tom’s CPU charts and see some direct comparisons between the 640 and 1055 CPUs : http://www.tomshardware.com/charts/desktop-cpu-charts-2010/benchmarks,112.html
The two video transcoding benchmarks are probably the most relevant to you.
Here is also a side by side comparison of all the benchmarks for those two chips: http://www.tomshardware.com/charts/desktop-cpu-charts-2010/compare,2424.html?prod=on&prod=on
How much are you really encoding and will it be the only think the computer is used for? the 1055 will consume considerably more electricity if the computer is left on 24/7 and if you are only encoding one video every other day, the added speed may not be worth it in the long run.
One last thing to consider is while these combo deals are tempting, they usually come with cheap parts. The 6-core system overall has better components such as the antec case, antec power supply, and Asus mobo. That alone may be worth the extra money. If you look at the pictures of the case with PSU on the quad core combo, it has a 115-230V red switch which usually means that the PSU is a lower end unit.