Would you please elaborate the statement that "the Interrupts are disturbed". Also, if you are using I2CHW module and I2CHW_fSendStart() and I2CHW_SendStop() API, then these APIs disable the I2C interrupt, so it needs to be enabled again and pending interrupts of I2C has to be cleared.
If you don't want this to happen then you can wait for some time to complete the write or read transaction. This can be done by a normal for loop.
Also, there is an example project on CY website which might be helpful to you. Here is the link for that project: http://www.cypress.com/?rID=34661 .
This might be too much late and you might have resolved your issue.
But as a standard firmware rule, interrupt routine should be as small as possible. So interrupt should not keep your CPU engage for most of the time and allow it to do other job.