Scott,
I am having the same problem with a reference design for a Spartan 3 Starter Brd.
The design was generated within EDK 8.2 and I am using 9.1.
When I initially opened the design, EDK took me through an update Wizard which updated some, but not all, of the design.
It left me with a log file, Version_Changes.log, which contained the following:
The following files will be modified:
system.mhs
system.mss
--------------------------------------
The following changes will be made:
Core opb_gpio 3.01.a will be replaced by 3.01.b
Core opb_v20 1.10.b will be replaced by 1.10.c
Driver cpu 1.00.a will be replaced by 1.01.a
Driver uartlite 1.00.b will be replaced by 1.02.a
--------------------------------------
The following changes need to be made manually by the user:
Core microblaze 2.10.a needs to be replaced by 6.00.b
Core lmb_bram_if_cntlr 1.00.b needs to be replaced by 2.00.a
Core opb_emc 1.10.b needs to be replaced by 2.00.a
Core fsl_v20 1.00.b needs to be replaced by 2.10.a
Driver emc 1.00.a needs to be replaced by 1.01.a
After much trial and error, mostly error, I edited the mhs and mss files to conform to the manuall changes indicated in the last section above.
The core instances were in the mhs file, and the driver instance was in the mss file.
While this got me further along, there is more to this equation and I am not yet done.
Good luck.
Mark Abraira