It's hard to define out what is the cause except .I 'll investigate it myself.
As you said that all PIN is held LOW. Is this mean SCL?

The SCL can be held low after each acknowledge ,if the slave device are
busy .This mean that you have to Poll the SCL until it release the clock
line (For software I2C).

It's not hard real-time but you 'd better take care of timing ,Other extra-approximate
timing should be taken place by interrupt only.