SDRAM issue - LPC1788
Smells like a data-dependent problem.  You may have some unfortunate coupling between some of the data and/or address lines such that the right pattern causes a failure somewhere.  

Try slowing down the clock.  How the symptom changes or not may give some clues.  If there is crosstalk between some of the address and data lines, this should make the problem go away because transfers are done after everything eventually settles.  If the problem is noise getting onto the clock line, then this probably won't change anything.

Look at some of the signals with a scope and see how clean they look.  Did you put resistors in series with the lines to match the trace impedance better and reduce ringing?  Make sure to check the clock line too, not just a few data lines.  Also verify you really have the setup and hold times the chip needs.

Remember that apparent proper operation is not proof of correct operation, only of being lucky.