If your test and your larger program give the same output that you've provided and then one passes and the other fails, then probably the issue is somwhere else. The configuration listed in your post looks good.The star at "*setupReal" looks suspicious. The difference between the test and larger problem may also be in the way they are linked with MKL.
When you do DftiGetValue(hand,DFTI_INPUT_STRIDES,array), make sure the size of the array is 1 more than the dimensionality of transform. In 1D case the array should be capable of holding two MKL_LONG items.
The same refers to DFTI_OUTPUT_STRIDES.