@franciscoklf

I have not run into this problem myself.

I am using Knoppix 6.2.1 installed from CD to a 2Gb USB card, with 1.1 Gb persistent.
My Synaptic uses default parameters except for repositories; I use only two, the 'stable'
ones, except for a few programs like LXDE, its lx-helpers, and flash.
I don't find _any_ apt.conf, as such, on my 6.2.1 setup.

FWIW, I don't attempt any massive upgrades with _all_ repos active.
I do comprehensive upgrades using the two stable repos with no problems.

In your Knoppix 6.2 case, the suggestion to increase the cache limit seems like a good
first step. If that doesn't work out, you might try Knoppix 6.2.1.
Beyond that, we probably ought to know more specifics about your pc.