NIOS is generating Read Signal Twice.

So, Nios 2 has a 32 bit read/write port (one for read and one for write) while your device has an interface with 16 bits on the avalon bus. This is a mismatch, the interconnect fabric in SOPC builder will split the read or the write in two. Take a look at http://www.altera.com/literature/manual/mnl_avalon_spec.pdf, paragraph 3.6.1

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For example, when a 32-bit master port

performs a read transfer from a 16-bit slave port, the system interconnect fabric

executes two read transfers on the slave side on consecutive addresses, and presents

32-bits of slave data back to the master port

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If I understood correctly your situation, this may be a good cause for reading twice.