There's several antivirus softwares that warns as soon as one program tries to modify an already existing file, as it thinks it could be placing malicious code in it. It probably depends of how the code is written, if it reads the whole file, modifies it and rewrite the whole file back, or if it uses a routine that only goes into an adress in the file and put some bytes there, which will raise a red flag.
/Ubbe