I am sorry that you felt my response was ignoring you, it was a reply to both posts. I sent you a PM explaining further.
Alg.exe is usually part of the Windows Internet Connection Sharing and Internet Connection Firewall. The "Internet" part of those names is misleading, these components monitor and affect ANY external connection made by your computer including local network connections, not just ones on the internet. Because of this all of the suggestions for checking the firewall apply to your issue.
Your Firewall is configured to allow FlashFXP to access the internet you said. What Firewall are you using? Do you have the Windows XP Firewall on as well? Have you checked if your Firewall has any sort of worm protection scanning it is doing of incoming files? Is there an Anti-virus program that may be doing scanning of files as they are incoming?
After checking out the firewall/anti-virus the next step would be to check if file compression is being used with these FTP transfers. Do you have compression turned on for the site you are connecting to, and if so does your FlashFXP session log show it is being used? File compression could cause a heavy resource use as files are uncompressed at the local level.
A third possible problem related the alg.exe is it is a filename that some worm/trojan/spywares will use, have you done any checks for these problems recently? If you turn off ICS and ICF but still have alg.exe using CPU time this is the most likely problem.
If all of these things are unsuccesful at finding the problem please post more information on your problem including a session log for one of these transfers and as complete of description of your system, security setup and network setup as possible.
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