NIOS II PIO Data read problem

First of all you must write ones, not zero, into edge capture register to reset status:

IOWR_ALTERA_AVALON_PIO_EDGE_CAP(STROBE_BASE, 1)

Anyway this seems to be irrelevant, unless you are using edge capture in another part of the code.

I guess your problem is that you can't get the correct pio status in 'data', isn't it?

This can be simply due to bad timing relative to strobe signal.