Could you please make sure whether the second argument passed to CyU3PConnectState() API is CyTrue, which enables SS enumeration.
I have already done that. I'm using the example code of "USBBulkLoopAuto".
I know this is a bit on the late side in terms of a response, but I have had reasonable success with the MSC and RAID examples. Both worked reasonably well out of the box. You won't see 350MBps out of the FX3S (and probably just barely with a FX3) because of limitations on the external buses. However you'll definitely be able to do more than over USB2. I really wish the FX3S would support a 200MHz MMC/SD clock, or at least do 100 at DDR.
The Pactron board is not the best place to start for GPIF experimentation, because it only exposes a few pins to the outside. If that's what you are after, it'd be a good idea to look at some of the FX3 boards (though they will lack the SD/MMC interface).
Generic tips for making things work: (1) don't change the GPIF configuration; the startup libraries do a lot of poorly/undocumented limitation checks and don't seem to handle all conditions gracefully (perhaps due to bugs, or undocumented hardware limitations). (2) double check IO assignments as the FX3 demo boards are different from the Pactron FX3S.
As a general statement the Cypress FX3 SDK could use some better out-of-the box support for examples, and get rid of the old versions of Eclipse and GCC. Both are doable (I'm running Eclipse Oxygen and GCC 7.2), but a bit painful at first. Cypress should also publish a full register set for the FX3/FX3S (there seems to be a good number of undocumented ones). And finally, if they were to publish the full source for their libraries I could fix what appear to be bugs in their code (e.g. the MMU configuration seems to be a bit funky).