To answer all the above questions :
1. All the PI values were taken at room temperature after thorough overhaul and dry out. (PI, in any case, is supposed to be temperature independent.)
2. Sufficient time gap was maintained between each phase test (remember, when one phase is tested, other two phases are grounded for at least ten minutes i.e. the time taken to measure the PI of the first phase + a discharge time of 10 minutes). After testing the individual phases, all the 3 phases were grounded for over 15 minutes, before measuring PI of the 3 phases together.
3. To reconfirm our test results, we did repeat the PI tests the next day with the same results (i.e, individual phases having a PI of over 2 and 3 phases together having only 1.1)
4. Since we had to ac hipot the windings at 16.5 KV (1.5 times the rated voltage), I took the above PI values. With the PI test results being a mystery, I chanced my arm and went ahead with successfully hipotting the individual phases at 16.5 KV with the same leakage current for all the 3 phases. The generator is online now.
I still haven't a clue to explain the above PI values, which I frankly admitted to my client.
Thank you guys for keeping this thread still alive and look forward to some satisfactory explanation.