Does anyone know why a project would be as detected as having a virus ?
I run the AVG 2013 free, and have run AVG free for quite a few years.

This is the 2nd time in about 2 weeks. (my scanner runs 3 times a week)
First time i removed it with the scanner, and let BONIC re-download what is needed.

Now this is happened again. (i do not know if it's the same file.
C:/ProgramData\BONIC\projects\milkyway.cs.rpi.edu_milkyway_separation_1.00_windows_intel86.exe

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This has happened before with AVG. You can either set it to ignore Boinc or try something else. It's why I switched to MSSE.

But i wonder what or why it is causes these alerts.

I use ESET Security 5...no issues here

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But i wonder what or why it is causes these alerts.

It is a false positive meaning it just thinks it found something, it didn't really find something. What is easiest is to just exclude the Boinc directory from the scans as a REAL virus will try to quickly spread to other parts of your pc and will then get caught. IF it IS a REAL virus and STAYS in the Boinc directory, who cares, it is the projects problem and they DO have better scanners than you and I do.

AV programs are trying to get better and better at predicting what a virus will do as it works it way thru your pc, this makes for some interesting algorithms that can also see non virus stuff as viruses. It would be sort of like most people that go Christmas Shopping, store security HATES that time of year as ALOT of people pick stuff up, put it down, walk to another place pick something up then put it down again, walk to someplace else etc, etc, etc. That IS all activity that is indicative of a shoplifter, but is ALSO indicative of someone looking for the PERFECT gift!