I forgot to ask you what specific build of v4.4 are you using?
Do you recall what version/build of FlashFXP you upgraded from?
All previous builds can downloaded from our website if you want to try an older release.
http://archive.flashfxp.com/archives/
I conducted some tests using the latest v4.4 build (2044) and based on the results I am not seeing anything abnormal about the cpu usage.
A few things to consider which might attribute to the high cpu load.
1. If the file being transferred is highly fragmented this can increase the time it takes for each read operation and can increase the cpu usage.
2. Windows Defender (or any anti-virus, malware scanner) with real-time protection/scanning can increase the cpu usage of the application that is accessing the file.
3. If too many programs are reading/writing to the drive where the file is located or if the drive contains a temp file such as windows pagesys.sys or hiberfil.sys this can create a bottleneck and increase cpu load.
4. Sometimes rebooting can resolve unusually high cpu load.