Control.com - Nerds in Control

First, sorry for my bad English, I am trying to improve my English.

We have a 3.3KV,485 KW submersible pump fed via a 11/3.3 KV transformer and protected with fuse and MICOM relay (p241). One month ago, we pulled it out from water for some mechanical job. They repaired the sealing of the motor. After they finished the job, they sent the pump down and we meggered the cable and motor. The megger shows only 10 kilo omhs! We had to start the pump! And we did! I expected that the pump would be gone immediately but it works well!!
After 14 days, when I was on vacation, MICOM relay tripped the pump because of sensitive earth fault. They started it again and after 9 seconds it went again due to sensitive earth fault. Megger test shows short circuit.

On the other hand, I saw the disturbances which are recorded by MICOM, it shows that sometimes the motor was working with 2 phase and one phase had zero current, (something likes loose connection). The question is, what happened? Zero current shows that one phase must be disconnected! But megger test shows that one phase or more phases are shorted. I am really confused!! Someone help me! Thanks.