The military Lockheed C-130 aircraft was tracking to Pearce from Edinburgh via reporting points BADJA and PEPPA, whilst an Avro RJ-70 was tracking from Perth to Telfa via CLIFY and PEPPA. The pilot of the C-130 had been cleared to descend to 8,000 ft by Perth ATC and the RJ-70 was on climb to FL290. However, the C-130 was observed on radar to drift south of track and then turn left prior to PEPPA. As a result of the early turn, the C-130 passed approximately 3 NM south of PEPPA. The C-130 crew could not recall why the aircraft had drifted south or turned early. However, it was reported that it was possible that the C-130's inertial navigation system (INS) may have experienced some drift. It was also reported that because the INS calculates an intercept to the next leg based on the aircraft's expected turn radius, it may have commanded a turn earlier than ATC expected. Perth ATC directed the pilot of the RJ-70 to turn the aircraft right to pass behind the crossing C-130. Just after the RJ-70 pilot gave his read-back to the instruction, he advised Perth ATC that he had received a TCAS alert. Perth ATC passed traffic and the two aircraft passed abeam each other at 4 NM with no vertical separation. There was a breakdown in separation as the required standard was 5 NM. Perth ATC reported that just prior to the incident, Pearce Control had experienced a radar failure. As a result, the Perth "Inner" air traffic controller, who was under training and being supervised at the time, experienced a substantial workload increase requiring him to scan a larger area than normal, thus changing his radar scan parameters. He also had 12 aircraft on frequency. The trainee air traffic controller's workload, whilst heavy, was not considered excessive because he had completed 4 weeks of the 6 week training course and was already an experienced procedural controller. Perth ATC reported that at 15 NM inbound to PEPPA, the C-130 had a groundspeed of 330 kts and the trainee controller assessed that the separation between the aircraft would be adequate. However, abeam PEPPA, the C-130's groundspeed unexpectedly reduced to 220 kts before increasing again to 255 kts. The speed changes may have been associated with the aircraft accelerating in the descent and then slowing following the level off. The C-130's unexpected speed changes and early turn near PEPPA adversely affected the trainee controller's planned separation between the two aircraft. The trainee had issued frequency transfer instructions to the pilot of the C-130 just before the impending breakdown in separation was noticed. Although the training officer assumed control of the position as the separation breakdown developed, he could only issue instructions to the pilot of the RJ-70. This limited the options available to the training officer when he was attempting to correct and avoid the separation breakdown. It is probable that the workload increase caused by the non-operative Pearce radar associated with the C-130's unexpected deviation from the air route and groundspeed changes, were factors in allowing the breakdown in separation to develop. When the training officer noticed the developing separation breakdown, his options in ensuring the required separation were limited by the C-130 being on another frequency.