I have this same problem while raiding. Target and target of target disappear. When solo, I noticed that target of target disappears sometimes. I'll try disabling Prat as well and see if that works for me.
The exact same behaviour occurs on my setup with ag_unitframes, so it might not be local to just Pitbull. I have Prat and the latest Bongos (not Bongos2) and I don't get frames either in the manner that you specified. Last night during a Gruul raid I thought ag_uf might be the culprit and disabled that and left Prat running. It wasn't interfering with the default Blizzard target/ToT frames. I'll try disabling Prat instead and see what happens.
TrinityBars was causing the problem for me with PitBull. Removing/Updating to the newest version of TrinityBars fixed it. Unsure if it will also fix ag but it seems like it's the same problem with both add-ons.