That is unexpected. v2.1.1 was a bug fix release for the powerUp & powerDown functions so I didn't realise I'd broken Due support. Thanks for the heads up - I'll test and get back to you with a fix shortly, however, for the time being, using v2.1.0 should solve the problem.
Update:
I've just tested my Due with v2.1.1 and the only issue I have with it is that powerDown() returns a false negative (This is being fixed in the upcoming v2.2.0). Everything else is functioning properly and returns the following:
Initialising Flash memory..........
----------------------------------------------------------------------------------------------------------------------------------
Get ID
----------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------
Manufacturer ID: efh
Memory Type: 13h
Capacity: 4014h
JEDEC ID: ef4014h
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Write Data
----------------------------------------------------------------------------------------------------------------------------------
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Data Written || Data Read || Result
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35 || 35 || Pass
-110 || -110 || Pass
4520 || 4520 || Pass
-1250 || -1250 || Pass
876532 || 876532 || Pass
-10959 || -10959 || Pass
3.1415 || 3.1415 || Pass
123 Test !@# || 123 Test !@# || Pass
Struct data written successfully
31325, 4.84, 880932, 1, 5
Saved!
Local values set to 0
After reading
31325, 4.84, 880932, 1, 5
Values from 0 to 255 have been written to the page 484
These values have been read back from page 484
Reading page (01e4)
000,001,002,003,004,005,006,007,008,009,010,011,012,013,014,015,
016,017,018,019,020,021,022,023,024,025,026,027,028,029,030,031,
032,033,034,035,036,037,038,039,040,041,042,043,044,045,046,047,
048,049,050,051,052,053,054,055,056,057,058,059,060,061,062,063,
064,065,066,067,068,069,070,071,072,073,074,075,076,077,078,079,
080,081,082,083,084,085,086,087,088,089,090,091,092,093,094,095,
096,097,098,099,100,101,102,103,104,105,106,107,108,109,110,111,
112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,
128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,
144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,
160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,
176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,
192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,
208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,
224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,
240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,
Have you tried running Diagnostic.ino - included in the examples after uncommenting #define RUNDIAGNOSTIC from the top of SPIFlash.cpp? (Make sure you save SPIFlash.cpp before you recompile and upload Diagnostics.ino) If you have, what errors did it print to your serial?
Can you post a photo of your wiring?
Also, if all fails have you tried using a different chip? I have previously found the chip returns 'busy' if the breadboard connections are not properly made or if the chip is faulty and not responding.