High cpu usage compared to what? A previous build, if so which build?
The most common cause of high cpu usage during upload is when the TCP/IP Buffer size is set too high. Default will provide the best speed/cpu usage for lan based transfers and increasing from default will typically increase cpu usage.
For high latency connections increasing the TCP/IP buffer size will not increase cpu usage.
This setting can be changed globally via the Preferences / Connection or per-site via the Site Manager.
update
While my results aren't exactly typical I can upload at 108 MB/s using direct gigabit PC to PC crossover cable with cpu usage around 5% on the first core (4-6% combined cpu).
When looking at cpu usage on a per-app basis its important to know how the application calculates the result, some process monitor applications will factor in system/hardware interrupts and this can double the cpu usage, especially if the file is extremely fragmented or if FlashFXP has to compete with other disk i/o operations.
The best two applications in my opinion are
Process Explorer or
Process Hacker, Now if you want to manage your processes and dynamically change their priorities based on the task at hand checkout
Process Lasso
