I have heard of problems with 2-way communication through an isolation transformer (On-Demand), and some channels are up in very high frequencies and can have problems through one.
My cable ground loop noise was much reduced by using an optical connection to my pre/pro instead of a digital coax.
I still had a little noise traveling from the cable box to the TV and back through various connections to the pre/pro.
I have wondered if using 3 isolation transformers on component video cables coming from the cable box might work. This, along with the optical cable, would move your 'blocking point' from just before the cable box to between the cable box and everything else.
As with anything, YMMV, the mentioned isolation products may work fine, I have not personally tried them.
Since I switched to FIOS I haven't had any ground loop noise, and I am using very efficient Zu Druids. I can't say if this is the nature of FIOS, if I the FIOS installer made sure to have a proper ground, or if I just got lucky. Fios is using the existing copper coax cable for in house distribution after the interface box in the garage.
Good Luck
Jason