Consider posting the PSOC 3 project so forum can take a look at whole
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Why did you step from PSoC4 to 3 and not to PSoC5? Both (4 and 5) have got a comparable core, an ARM, while the PSoC3 is equipped with the a bit old-fashioned 8051 core.
The warnings about the multiple calls come from the unique 8051 problems. I would suggest you to at least for testing to switch to a PSoC5 device and run a compile.