Ok, following is what I did in an effort to solve the problem.

1. A clean OS installation (I had to do it anyway, sooner or later, I wouldn't do it just because of the Java piece of Junk, only I think imho that JD will never be perfect as long as it relies on Java to function..);
2. Installed Java latest version.

A couple of things I noticed before doing these steps were:

-JD2beta was "resetting" entire rar packets I had previously downloaded.. once I could find them downloaded if I later opened the column by collapsing it (+ button), surprise!, all packets back to 0% from 100%.. (not always but often enough..:angry:);
-I found two javaw processes running at the same time, one going up to ~400 Mb and the other being normal (low) as far as required Ram resources.

Ok, yesterday was the first night JD2 didn't freeze.. I found only one (!) Java process running and everything seems to work much better now.

I will return to you guys in case something will be back in malfunction, but hopefully I found what it was to cause the problem!