Forgot to add that when I import the OFX after the manual schedule entry is done from the scheduled transactions window, the amounts match as expected, and the splits are not modified.
That makes sense. When you enter a schedule manually, the distribution of interest and amortization will be calculated based on the account balances. Then the transaction is entered into the ledger. When then the OFX import happens, a matching transaction is located based on the amount of the payment (single split) and the previously entered one (with three splits) is found and both are matched.
When you import the OFX in the other case, no matching transaction is located and the transaction is entered as is (that modifies the account balance of course). Then the schedules are searched for a matching one and only then the distribution is calculated. I assume the problem in that area though I cannot explain it based on the information @tcpsorcerer provided above.
The code is part of the MyMoneyStatementReader which is processing the OFX file and starts here.
Sample data showing the problem would be of great help now.