I don't think this helps. There's no way to tell if the PSoC is actually clock stretching because there's no way to tell who's pulling the clock line low.
What I would like to know is why are some options greyed out in the config window in one project, but available in the other project?
I think this is because 'wakeup from sleep' is not supported for your PSoC5 device (only with the upcoming PSoC5 LP), and the 'PinConnection' are only needed for this. (Look at the data sheet for an explanation of these 2 options).
(But if I'm right with that, the 'wakeup from sleep' checkbox should be enabled on the PSoC3 device, which it isn't. But this could also be because your I2C pins are not connected to the right pins)
I finally discovered the real reason it was working with the PSoC5 and not the PSoC3. Speed.
1) The PSoC5 defaults for a 48MHz main clock, while the PSoC3 is 24MHz.
2) Selecting 150kbps speed for the I2C was not enough, even though the I2C clocks at exactly this speed. I had to set it to 300kbps.
Many thanks for your time.