Something to consider here - because of the uncertainties in HF propagation, you can't be at all sure, from sitting at the spot where you are receiving, how the Shanwick controller is being received at the aircraft. He may well be coming in weak and covered with noise, much like the aircraft is apparently being received - essentially unreadable - at your end.
So I don't know if your statement that it was "scary" that the crew couldn't understand "plain instructions" was an implication that there was some incompetence there in the cockput, but put it this way: if all you could hear was something like what was coming back from the airplane (e.g. essentially a nearly unreadable signal-to-noise ratio), you might well transmit "in the blind" and just repeat your current flightplan back to them, just to try to be sure they had your current flightplan confirmed.
Propagation changes often, sometimes by the minute, so it may be that a few minutes later, the propagation path shifted just so, so that they were able to read Shanwick well enough to finally understand the instructions.
I can't say this was the scenario for sure, but likewise, we also don't know with any certainty that they were able to receive those "plain instructions" with any decent readability in the cockpit.
(Since you talked about using a "cheapo" SDR, can I assume you're using one of those DVB-T USB sticks with an RTL2832 device in it? If so, what are you using for an up-converter from HF into the VHF passband of the tuner device? One of those homebuilt NE-602-based mixers?)