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This problem should not have occurred because once the I2C UM is placed it will be listed in the devices provided interrupts are enabled. Since, you are using System Level Design, so this thing is taken care of automatically. Please zip your project and attach it here.
I'm having a similar problem,
Im using the 24894 with I2C on the ISSP pins,
Capsense with 16 buttons works fine transmitting the 16 raw values (12bit) if im using the CSD with PRS8 as clock source.
But if i use PRS16 or PRS8 with Prescaler the I2C bus never communicates.
With a demo board I ran into the same problem (well I think it was) a while back with the Bootloader I2C UM, I remember changing the I2C port to the other one (forget which one) and it worked.
I have tried starting from scratch but no luck.
I want more Resolution...
I'll provide you an example project and let me know if that helps or not
In addition, I've just noted that changing the Module from PRS8 (working fine) to PRS16 (I2C dies) and back to PRS8 does not revive the I2C...
I'm not changing anything else but the Module using Right Click on UM -> Selection Options...
I ran a file differences check and notices Port 1 (where my I2C is was being set up differenly after changing the CSD Module)
The PSoC Designer still had the port on the screen labled, but in the properties it had reverted back to default, so my I2C SCL pin was not working at all.
So i changed the EzI2C Pin parameter to the other port, then back again, and it fixed the problem.