Hi kraada and thanks to you too for your reply.
Ok, I decided to repeat the process. Started with updating my AV program to the latest definitions. Downloaded a fresh installation file for version 4.02.1. Installed it and got the same alert regarding TiltCommunicator.pt3. Reinstalled version 4.02 after this, but this time I got an alert on this version too. The file in question for version 4.02 was StarsCommunicator.pt4, so I'm pretty sure now that it is the AV program that has the problem.
There is just one more thing I need to check. To be able to install the program, I needed to turn off real-time scanning. I also made an exclusion regarding scanning for the files in question after it was installed. Now I'm able to look at the files and I see that those two files have a changed date 28.07.2012 15:29 and 28.07.2012 15:30 while for example the file BodogCommunicator.pt3 has a changed date 03.12.2011 00:41. Not sure if that mean the files has actually been changed or it is just because BodogCommunicator.pt3 was not included in the new installation package? Also could it be possible that I have some kind of virus on my pc that hooks up to those two files when I install the new package?
PS! When I install a new version, isn't that the same as reinstalling PT4 on top of my current installation?