We sign our installers and software with a secure code signature, so it can not be tampered with.... and it is virus free.
However virus checking programmes no longer just detect viruses. They have a database of every file they have come across.
If they find a file that they haven't seen thousands of (I don't know the exact numbers) they flag what is called a 'reputation' threat. Symantec for example show the threat name is ‘WS.Reputation.1
It doesn’t mean it has found a virus. It just means they haven't seen that many copies.
For small time applications like ChimpySync – it takes us a while to get to thousands of downloads… and then when we have to release a new version we start the count all over again. We used to be able to whitelist installation files, but virus programmes no longer seem to allow that.
Our code is signed with a securecode signature, so it can’t be tampered with. You should be able to rightclick (or similar) and tell your virus programme to install anyway.