hi funny you brought this up, becuase i thought of removing flashing some days ago.
I really cant understand your problem tough, i think it is FTP thats needs some altering, have you looked in Options for something like "bring to top" checkbox?
Quote:
Taskbar alerts
When a window is opened it will either appear over an existing window or it will appear minimised on the toolbar and flash when it’s available to use. This Registry alteration will enable you to control this behaviour. It’s ideal for dealing with pop-up windows, and will enable you to keep them on the Taskbar rather than having them obscure whatever you’re looking at. There are two settings to adjust depending on which way you want new windows to appear. The first controls the way in which a new window appears. Go along to HKEY_CURRENT_USER \ Control Panel \ Desktop and create a DWORD value called ForegroundLockTimeout, or modify the existing one. The value that you give it will determine the amount of time the new window appears over the old one. Enter a value of 0 and the new window will go over the top immediately. Enter the default value of 200000 (0x00030d40 hex) and the new window will appear on top for 200,000 milliseconds and then minimise to the Taskbar where it will flash. This flashing is controlled by the next tweak which will set the number of flashes. Create or modify the DWORD value ForegroundFlashCount and set a value for the number of flashes you require. 0 will make it flash infinitely or you can go for the default value of 3.
If the problem is that you just dont want the flashing at windows i think it needs investigating windowmessages because i didnt find any info on it on google or microsoft. I cant find the right one to tell the flash to stop in a specific window without to make it active
wParam 0x8006 is for when flashing starts