freeware & viruses
Some virus-scanning software have problems with executables that were shrunk with a tool called UPX. They wrongly report some of these files to contain a trojan horse.
UPX is freeware and therefore also is used by virus programmers. When an update for a virus scanner is written, it is not always easy, when dissecting a virus, to tell what is UPX and what is evil virus code. (Interestingly enough, it is mostly the smaller virus programs that have that problem.)
Programs by blechtrottel.net, too, can wrongly be accused. This is no reason for discomfort, most of the time you only need an update of the virus program in order to get rid of the bug. If you have doubts, simply check the file in question with a second (big) virus scanner.
Even very prominent programs sometimes have to cope with this phenomen. See this report at Total Commander from 3/1/2007.