We have used non-equilibrium phonon pulses to mimic X-ray photon absorption in a high quality Ta superconducting tunnel junction at 20 mK. From pulse shape measurements the charge output and decay time were determined. Values obtained were in good agreement with those obtained by photo-absorption after allowance for loss due to flux trapping, Results obtained for the quasiparticle loss rate due to Abrikosov vortices (fluxoids) were compared with the trapping model of Golubov and Houwman. Comparison of Ta and Nb results suggest that at very low temperatures fluxoid trapping may result in enhanced tunnelling rather than extra loss.