Humm, this looks strange. I've been modding BF1942, BF2 and IL-2 1946 with multiple mods (BF1918, FH, FH2, PR:BF2, VPModPack) in multiple computers using different OS, and never got such warnings.
You might want take a look at your anti-virus and other security configs. Some of them can be a real PITA and keep telling you everything you install on your rig is a "virus". Norton and McAfee are notable for such behavior.
Hope you get everything running safe and sound!
Best regards,
batistadk