I have exactly the same problem...
With the help of ebook Virtex5 FPGA Configuration User Guide I can "decompile" the encrypted bitstream to something like this... (NOPs arent shown)
0x0000012f: P1 WRITE CBC [30016004](4) 50 66 d8 9e f6 17 2c f8
49 ee 41 6b 3a de 6d de
0x00000143: P1 WRITE FDRI [30004000](0)
0x00000147: P2 WRITE [5003fd28](261416)
0x000ff60f: P1 WRITE CRC [30000001](1) 83 96 e4 9f
I can see, that iv has the same value like that one in my .nky file (Key StartCBC 5066d89ef6172cf849ee416b3ade6dde;) and if I decrypt data part (with AES-256 mode CBC) from offset 0x0000014b, size 261416 * 4 Bytes with key from .nkey file, I get something like this 09 95 2D 5B D0 E3 D0 19 ..., that doesnt looks like a valid data, so I made another encrypted bitstream (with different key and iv). The encrypted bitstreams are different only in date, iv, crc and of course encryped data. But, when I decrypt data part of the second bitstream with his iv and key, I get different output (A5 7E F8 8A AC 74 30 F6 ...). So I think that you dont use the standard NIST C AES 256 CBC, if you would, then I should get same output from the 1. and 2. bitstream.
And another thing, how are you computing crc, is it standard crc-32? after this command, crc is cleared,
0x00000097: P1 WRITE CMD [30008001](1) 00 00 00 07 Reset crc
and which data from the following bistream part are involved?
0x000000a7: P1 WRITE TIMER [30022001](1) 00 00 00 00
0x000000af: P1 WRITE ??? [30026001](1) 00 00 00 00
0x000000b7: P1 WRITE COR0 [30012001](1) 00 00 31 e5
0x000000bf: P1 WRITE COR1 [3001c001](1) 00 00 00 00
0x000000c7: P1 WRITE IDCODE [30018001](1) 02 86 e0 93
0x000000cf: P1 WRITE CMD [30008001](1) 00 00 00 09 Switch clk
0x000000db: P1 WRITE MASK [3000c001](1) 00 40 04 40
0x000000e3: P1 WRITE CTL0 [3000a001](1) 00 40 04 40
0x000000eb: P1 WRITE MASK [3000c001](1) 00 00 00 00
0x000000f3: P1 WRITE CTL1 [30030001](1) 00 00 00 00
0x0000011b: P1 WRITE FAR [30002001](1) 00 00 00 00
0x00000123: P1 WRITE CMD [30008001](1) 00 00 00 01 Write CFG
0x0000012f: P1 WRITE CBC [30016004](4) 50 66 d8 9e f6 17 2c f8
49 ee 41 6b 3a de 6d de
0x00000143: P1 WRITE FDRI [30004000](0)
0x00000147: P2 WRITE [5003fd28](261416)
0x000ff60f: P1 WRITE CRC [30000001](1) 83 96 e4 9f
Whole packets with their heads (30022001 00 00 00 00) or only the data parts (00 00 00 00) and what about NOPs (20 00 00 00) are they involved?
I was trying to compute crc from all data, all data w/o nops, only the data parts but with no luck...
Antonin Kriz