Apart from function of GPIO, PE[2:0] can also be used as GPIF debug pins or Timer 2,1,0 overflow output signal. Please note that the only one function of these three can be made available.
More information of altenate functions of Port E registers can be found in section 13.4.4 Port E Alternate Functions of the technical reference manual in the link http://www.cypress.com/?rID=38232
When the FX2 is in GPIF mode, PortE[2:0] can be used for GPIO purposes, or act as the GSTATE debug outputs that reflect the state of the GPIF engine. This is very useful for debugging GPIF applications. T0-2OUT functionality is multiplexed with PortE[2:0] and used for output signals that indicate when the Timer 0-2 count overflows. These output signals only last for one CLKOUT cycle.