IRtool is really old; use IrScrutinizer instead.  However, that will tell you that the IR protocol is not recognized.  I can tell you that the signals are not even remotely close to NEC format.

In any event, to make PEP understand the last set of Pronto Hex, change
0000 0058 0000 0054
to 
0000 0058 0000 002B